Materials and methods for using an acyl-acyl carrier protein thioesterase and mutants and chimeras thereof in fatty acid synthesis

ABSTRACT

A method of increasing production of fatty acids comprising introducing into a host cell or organism and expressing therein an acyl-acyl carrier protein (ACP) thioesterase (TE) from  Bryantella formatexigens  or a mutant thereof; a method of making a mutant  B. formatexigens  acyl-ACP TE; a method of making a chimeric  Cuphea viscosissima  acyl-ACP TE; a nucleic acid encoding a mutant acyl-ACP TE or a chimeric  C. viscosissima  acyl-ACP TE; a host cell or organism comprising the nucleic acid; a mutant acyl-ACP TE or chimeric  C. viscosissima  acyl-ACP TE; a method of altering the specificity of a plant acyl-ACP TE; and a method of altering the level of activity of a plant acyl-ACP TE.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority to U.S. provisional patent applicationNo. 61/512,373, which was filed on Jul. 27, 2011, and is herebyincorporated by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

The work described herein was supported, at least in part, by TheNational Science Foundation under contract no. EEC0813570. Therefore,the Government of the United States of America has certain rights in theinvention.

TECHNICAL FIELD

The present disclosure relates to enzymes, mutants and chimeras thereof,fatty acid synthesis, nucleic acids, proteins and host cells andorganisms.

BACKGROUND

De novo fatty acid biosynthesis can be considered an iterative“polymerization” process, commonly primed with the acetyl moiety fromacetyl-CoA and with iterative chain extension occurring by reaction withmalonyl-acyl carrier protein (ACP). In most organisms this processoptimally produces 16- and 18-carbon (C16 and C18) fatty acids. Theenzyme that determines fatty acid chain length is acyl-ACP thioesterase(TE). This enzyme catalyzes the terminal reaction of fatty acidbiosynthesis, acyl-ACP thioester bond hydrolysis (i.e., the hydrolysisof the thioester bond between the acyl chain and the sulfhydryl group ofthe phosphopantetheine prosthetic group of ACP), to release a free fattyacid and ACP. This reaction terminates acyl-chain elongation of fattyacid biosynthesis and, therefore, determines fatty acid chain length. Itis also the biochemical determinant of the fatty acid composition ofstorage lipids in plant seeds.

In discrete phyla and/or tissues of specific organisms (primarily higherplant seeds), thioester hydrolysis optimally produces medium-chain(C8-C14) fatty acids (MCFAs), which have wide industrial applications(e.g., producing detergents, lubricants, cosmetics, and pharmaceuticals)(Dehesh et al., Plant Physiol. 110: 203-210 (1996)). TEs thatspecifically hydrolyze medium-chain acyl-ACP substrates have beenstudied widely (Dehesh et al. (1996), supra; Voelker et al., Science257: 72-74 (1992)); and Yuan et al., PNAS USA 92: 10639-10643 (1995)).Short-chain fatty acids (SCFAs; e.g., butanoic acid and hexanoic acid)have more recently gained importance as potential bio-renewablechemicals that could be derived from the fatty acid biosynthesis pathway(Nikolau et al., Plant J. 54: 536-545 (2008)). As a critical acyl chaintermination enzyme, acyl-ACP TEs with desired substrate specificitiesare, therefore, important for engineering this pathway.

To date, dozens of acyl-ACP TEs have been functionally characterized andsorted into two classes, FatA and FatB (Jones et al., Plant Cell 7:359-371 (1995)). FatA-class TEs act on long-chain acyl-ACPs,preferentially on oleoyl-ACP (Jones et al. (1995), supra; Hawkins etal., Plant J. 13: 743-752 (1998); Serrano-Vega et al., Planta 221:868-880 (2005); and Sanchez-Garcia et al., Phytochemistry 71: 860-869(2010)), while FatB-class TEs preferably hydrolyze acyl-ACPs withsaturated fatty acyl chains (Jones et al. (1995), supra). Thearchetypical FatB-class TE was isolated from the developing seeds ofCalifornia bay (Umbellularia californica). This enzyme is specific for12:0-ACP, and it plays a critical role in MCFA production (Voelker etal. (1992), supra; and Pollard et al., Arch Biochem. Biophys. 284:306-312 (1991)). This discovery spurred isolation of additionalMCFA-specific TEs from Cuphea (Dehesh et al. (1996), supra; Dehesh etal. Plant J. 9: 167-172 (1996); and Leonard et al., Plant Mol. Biol. 34:669-679 (1997)), Arabidopsis thaliana (Dormann et al., Arch Biochem.Biophys. 316: 612-618 (1995)), Myristica fragrans (nutmeg) (Voelker etal., Plant Physiol. 114: 669-677 (1997)), and Ulmus americana (elm)(Voelker et al. (1997), supra).

Recently, TEs obtained from public databases were classified into 23families based on sequence and three-dimensional structure similarity(Cantu et al., Protein Sci. 19: 1281-1295 (2010)). These TEs weredefined as enzymes that can hydrolyze any thioester bond irrespective ofthe chemical nature of the carboxylic acid and thiol molecules thatconstitute the substrates of these enzymes. The TE sequences arecollected in the constantly updated ThYme database(www.enzyme.cbirc.iastate.edu; Cantu et al., Nucleic Acids Res. 39:D342-346 (2011), which is hereby incorporated by reference). Of these 23families, Family TE14 contains plant and bacterial acyl-ACP TEs involvedin Type II fatty acid synthesis, the reactions of which are catalyzed bydiscrete mono-functional enzymes. Family TE14 contained 360 uniquesequences as of late 2010, but only ˜7% of these sequences had beenfunctionally characterized, and all of those were FatA and FatB TEs fromhigher plants. The remaining ˜220 bacterial acyl-ACP TEs were mostlygenerated from genomic sequencing projects and had not been functionallycharacterized.

Alteration of the substrate specificity of plant TEs has been describedby Yuan et al. (U.S. Pat. Nos. 5,955,329 and 6,150,512, which areincorporated herein by reference for their teachings regarding same) andRoessler et al. (U.S. Pat. App. Pub. No. 2011/0020883, which is herebyincorporated by reference for its teachings regarding same). Yuan et al.identifies the C-terminal two-thirds portion of plant TEs as desirablefor modification. Roessler et al. discloses a plant acyl-ACPthioesterase of a specified sequence (sequence identification no. 29) inwhich amino acid 174, alone or in further combination with amino acid103, is mutated.

In view of the foregoing, the present disclosure seeks to providemethods of using acyl-ACP TE and mutants and chimeras thereof, inparticular bacterial and plant acyl-ACP TE and mutants and chimerasthereof, to alter substrate specificity and/or alter activity (e.g.,increase production of fatty acids) in a host cell or organism. Theseand other objects and advantages, as well as additional inventivefeatures, will become apparent from the detailed description providedherein.

SUMMARY

A method of increasing production of fatty acids, such as short-chainfatty acids and/or fatty acids having from about six carbons to about 12carbons, such as from about 10 carbons to about 12 carbons (e.g., fattyacids having less than about 10 carbons or fatty acids having less thanabout 12 carbons) in a host cell or organism is provided. The methodcomprises introducing into the host cell or organism and expressingtherein a nucleic acid molecule comprising a nucleotide sequenceencoding an acyl-acyl carrier protein (ACP) thioesterase (TE) fromBryantella formatexigens.

Another method of increasing production of fatty acids, such asshort-chain fatty acids and/or fatty acids having from about six carbonsto about 12 carbons, such as from about 10 carbons to about 12 carbons(e.g., fatty acids having less than about 10 carbons or fatty acidshaving less than about 12 carbons) in a host cell or organism is alsoprovided. The method comprises introducing into the host cell ororganism and expressing therein a nucleic acid molecule comprising anucleotide sequence encoding a mutant acyl-ACP TE derived from wild-typeBryantella formatexigens acyl-ACP TE, wherein the mutant acyl-ACP TEproduces more fatty acids, such as short-chain fatty acids, in the hostcell or organism that the corresponding wild-type acyl-ACP TE.

Also provided is a method of making a mutant Bryantella formatexigensacyl-ACP TE. The method comprises making a mutant Bryantellaformatexigens acyl-ACP TE comprising two or more amino acid mutationscomprising N169Y and S222I.

An isolated or purified nucleic acid molecule is also provided. Thenucleic acid molecule comprises a nucleotide sequence encoding a mutantacyl-ACP TE, which is derived from wild-type Bryantella formatexigensacyl-ACP TE, comprises two or more amino acid mutations comprising N169Yand S222I, and has increased thioesterase activity compared to wild-typeBryantella formatexigens acyl-ACP TE. The isolated or purified nucleicacid molecule can be a vector.

Also provided is a host cell or organism. The host cell or organismcomprises the above-described nucleic acid molecule comprising anucleotide sequence encoding a mutant acyl-ACP TE.

Further provided is an isolated or purified mutant acyl-ACP TE. Themutant acyl-ACP TE is derived from wild-type Bryantella formatexigensacyl-ACP TE, comprises two or more amino acid mutations comprising N169Yand S222I, and has increased thioesterase activity compared to wild-typeBryantella formatexigens acyl-ACP TE.

A method of making a chimeric Cuphea viscosissima acyl-ACP TE gene isalso provided. The method comprises replacing a segment of a wild-typeCuphea viscosissima acyl-ACP TE with a segment of another acyl-ACP TE.

Further provided is another isolated or purified nucleic acid molecule.The nucleic acid molecule comprises a nucleotide sequence encoding achimeric Cuphea viscosissima acyl-ACP TE gene, which comprises a segmentof another acyl-ACP TE gene. The isolated or purified nucleic acidmolecule can be a vector.

Still further provided is another host cell or organism. The host cellor organism comprises the above-described isolated or purified nucleicacid molecule comprising a nucleotide sequence encoding a chimericCuphea viscosissima acyl-ACP TE gene.

Even still further provided is an isolated or purified chimeric Cupheaviscosissima acyl-ACP TE. The chimera comprises a segment of anotheracyl-ACP TE.

A method of altering the specificity of a plant acyl-ACP TE for at leastone of its substrates is also provided. The method comprises introducinginto the plant acyl-ACP TE a substrate specificity-altering mutation inthe region corresponding to amino acids 118-167 of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2. Themethod can comprise mutating at least one amino acid corresponding to anamino acid selected from the group consisting of amino acid 133, aminoacid 142, and amino acid 143 of the mature amino acid sequence of theCuphea viscosissima acyl-ACP TE encoded by FatB2. The method can furthercomprise mutating at least one amino acid corresponding to an amino acidselected from the group consisting of amino acid 110 and amino acid 184of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2. The method can further comprise altering the level ofactivity of the plant acyl-ACP TE by a method comprising mutating atleast one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 173, amino acid 176, and amino acid 205of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2.

In view of the foregoing, a method of altering the level of activity ofa plant acyl-ACP TE is also provided. The method comprises mutating atleast one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 173, amino acid 176, and amino acid 205of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2. The method can further comprise altering thespecificity of the plant acyl-ACP TE by a method comprising introducinginto the plant acyl-ACP TE a substrate specificity-altering mutation inthe region corresponding to amino acids 118-167 of the mature amino acidof the Cuphea viscosissima acyl-ACP TE encoded by FatB2. The method cancomprise mutating at least one amino acid corresponding to an aminoselected from the group consisting of amino acid 133, amino acid 142,and amino acid 143 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The method can furthercomprise mutating at least one amino acid corresponding to an amino acidselected from the group consisting of amino acid 110 and amino acid 184of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2.

Yet another isolated or purified nucleic acid molecule is provided. Theisolated or purified nucleic acid molecule comprises a nucleotidesequence encoding a mutant plant acyl-ACP TE, which comprises asubstrate specificity-altering mutation in the region corresponding toamino acids 118-167 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The isolated or purifiednucleic acid molecule can be a vector. The encoded mutant plant acyl-ACPTE can comprise a mutation of at least one amino acid corresponding toan amino acid selected from the group consisting of amino acid 133,amino acid 142, and amino acid 143 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2. The encoded mutantplant acyl-ACP TE can further comprise a mutation of at least one aminoacid corresponding to an amino acid selected from the group consistingof amino acid 110 and amino acid 184 of the mature amino acid sequenceof the Cuphea viscosissima acyl-ACP TE encoded by FatB2. The encodedmutant plant acyl-ACP TE can further comprise a level ofactivity-altering mutation of at least one amino acid corresponding toan amino acid selected from the group consisting of amino acid 173,amino acid 176, and amino acid 205 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2.

Still yet another isolated or purified nucleic acid molecule isprovided. The isolated or purified nucleic acid molecule comprises anucleotide sequence encoding a mutant plant acyl-ACP TE, which comprisesa level of activity-altering mutation of at least one amino acidcorresponding to an amino acid selected from the group consisting ofamino acid 173, amino acid 176, and amino acid 205 of the mature aminoacid sequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.The isolated or purified nucleic acid molecule can be a vector. Theencoded mutant plant acyl-ACP TE can further comprise a substratespecificity-altering mutation in the region corresponding to amino acids118-167 of the mature amino acid of the Cuphea viscosissima acyl-ACP TEencoded by FatB2. The encoded mutant plant acyl-ACP TE can comprise amutation of at least one amino acid corresponding to an amino acidselected from the group consisting of amino acid 133, amino acid 142,and amino acid 143 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The encoded mutant plantacyl-ACP TE can further comprise a substrate specificity-alteringmutation of at least one amino acid corresponding to an amino acidselected from the group consisting of amino acid 110 and amino acid 184of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2.

Another host cell or organism is provided. The host cell or organismcomprises the above-described isolated or purified nucleic acid moleculecomprising a nucleotide sequence encoding a mutant plant acyl-ACP TE,which comprises a substrate specificity-altering mutation in the regioncorresponding to amino acids 118-167 of the mature amino acid sequenceof the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

An isolated or purified mutant plant acyl-ACP TE is also provided. Theisolated or purified mutant plant acyl-ACP TE comprises a substratespecificity-altering mutation in the region corresponding to amino acids118-167 of the mature amino acid sequence of the Cuphea viscosissimaacyl-ACP TE encoded by FatB2. The mutant TE can comprise a mutation ofat least one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 133, amino acid 142, and amino acid 143of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2. The mutant TE can further comprise a substratespecificity-altering mutation of at least one amino acid correspondingto an amino acid selected from the group consisting of amino acid 110and amino acid 184 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The mutant TE can furthercomprise a level of activity-altering mutation of at least one aminoacid corresponding to an amino acid selected from the group consistingof amino acid 173, amino acid 176, and amino acid 205 of the matureamino acid sequence of the Cuphea viscosissima acyl-ACP TE encoded byFatB2.

Yet another isolated or purified mutant plant acyl-ACP TE is provided.The isolated or purified mutant plant acyl-ACP TE comprises a level ofactivity-altering mutation of at least one amino acid corresponding toan amino acid selected from the group consisting of amino acid 173,amino acid 176, and amino acid 205 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2. The mutant TE canfurther comprise a substrate specificity-altering mutation in the regioncorresponding to amino acids 118-167 of the mature amino acid of theCuphea viscosissima acyl-ACP TE encoded by FatB2. The mutant TE cancomprise a mutation of at least one amino acid corresponding to an aminoacid selected from the group consisting of amino acid 133, amino acid142, and amino acid 143 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The mutant TE can furthercomprise a substrate specificity-altering mutation of at least one aminoacid corresponding to an amino acid selected from the group consistingof amino acid 110 and amino acid 184 of the mature amino acid sequenceof the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a sequence alignment of deduced amino acid sequences of C.nucifera (Cn) (CnFatB2 [SEQ ID NO: 4], CnFatB1 [SEQ ID NO: 5], andCnFatB3 [SEQ ID NO: 6]) and C. viscosissima (Cv) (CvFatB1 [SEQ ID NO:2], CvFatB2 [SEQ ID NO: 3], and CvFatB3 [SEQ ID NO: 1]) acyl-ACP TEs.The putative N-terminal amino acid residue of the mature protein isleucine (▾). Two arrows indicate the conserved regions from which thedegenerated primers were designed. The N-terminal sequence of CvFatB2 isincomplete (*).

FIG. 2 a is a bar graph showing the fatty acid composition of E. coliK27 cultures expressing acyl-ACP TE from C. viscosissima or Cupheapalustris (Subfamily A). In parentheses are the organism and thesubfamily to which each sequence belongs. Error bars represent standarderrors.

FIG. 2 b is a bar graph showing the fatty acid composition of E. coliK27 cultures expressing acyl-ACP TE from U. Americana, I. germanica, orS. bicolor (Subfamily A). In parentheses are the organism and thesubfamily to which each sequence belongs. Error bars represent standarderrors.

FIG. 2 c is a bar graph showing the fatty acid composition of E. coliK27 cultures expressing acyl-ACP TEs from C. nucifera or E. guineensis(Subfamily A). In parentheses is the organism and the subfamily to whicheach sequence belongs. Error bars represent standard errors.

FIG. 2 d is a bar graph showing the fatty acid composition of E. coliK27 cultures expressing acyl-ACP TEs from P. patens (Subfamily B), S.bicolor (Subfamily B), or M. pusilla (Subfamily D). In parentheses arethe organism and the subfamily to which each sequence belongs. Errorbars represent standard errors.

FIG. 3 a is a bar graph showing the fatty acid composition of E. coliK27 cultures expressing acyl-ACP TEs from B. fragilis, P. distasonis, orB. thetaiotaomicron (Subfamily F). In parentheses are the organism andthe subfamily to which each sequence belongs. Error bars representstandard errors.

FIG. 3 b is a bar graph showing the fatty acid composition of E. coliK27 cultures expressing acyl-ACP TEs from S. dysgalactiae, L. brevis, orL. plantarum (Subfamily J). In parentheses are the organism and thesubfamily to which each sequence belongs. Error bars represent standarderrors.

FIG. 3 c is a bar graph showing the fatty acid composition of E. coliK27 cultures expressing acyl-ACP TEs from A. tetradius, B.Bacteriovorus, or C. thermocellum (non-grouped). In parentheses is theorganism for each sequence. Error bars represent standard errors.

FIG. 3 d is a bar graph showing the fatty acid composition of an E. coliK27 culture expressing C. perfringens (Subfamily G), C. asparagiforme(Subfamily H), Geobacillus sp. (Subfamily I), D. vulgaris (Subfamily E),or B. formatexigens (Subfamily H). In parentheses are the organism andthe subfamily to which each sequence belongs. Error bars representstandard errors.

FIG. 4 a is a gas chromatogram of an extract from E. coli K27 cultureexpressing a bacterial TE (Bdellovibrio bacteriovorus,GenBank:CAE80300).

FIG. 4 b is a gas chromatogram of the 2-tridecanone standard.

FIG. 4 c is a gas chromatogram of a mixture of the extract of FIG. 4 aand the standard of FIG. 4 b.

FIG. 4 d is a mass spectrum of 2-tridecanone.

FIG. 5 is a hierarchical clustering dendrogram of acyl-ACP TEs. Theacyl-ACP TEs are identified by their GenBank Accessions. Clusteranalysis was performed with fatty acid composition data using Euclideandistances and Ward's hierarchical clustering method. The p-values werecalculated via multiscale bootstrap resampling with 1,000 replicates.The Subfamily to which each sequence belongs is indicated inparentheses. Non-grouped sequences are indicated by asterisks.

FIG. 6 is a bar graph showing total activity of wild-type acyl-ACPthioesterase from Bryantella formatexigens (EET61113) and mutantsthereof. The data of all mutants (blue bars) were from single analyses,while the activity of wild-type was the average of 16 replicates.

FIG. 7 is a sequence alignment of deduced amino acid sequences of C.viscosissima (Cv) (CvFatB1 [amino acids 107-408 of SEQ ID NO: 2],CvFatB2 [amino acids 103-404 of SEQ ID NO: 3] and the strategy togenerate chimeric TEs. Arrows indicate the positions where the primerswere designed. Sequences for these primers are listed in Table 2. Thefragments I-VI are defined by the amino acid numbers in parentheses.

FIG. 8 a shows the mole percentage of individual fatty acids (FAs) from4:0 to 16:1 as well as the total FAs (μM) for each of six chimeric TEs(i.e., rTE3, rTE12, rTE48, rTE15, rTE51, and rTE60) and C. viscosissimaFatB1 (CvB1) and FatB2 (CvB2).

FIG. 8 b shows the mole percentage of individual fatty acids (FAs) from4:0 to 16:1 as well as the total FAs (μM) for each of 13 chimeric TEs(i.e., rTE4, rTE8, rTE16, rTE20, rTE24, rTE28, rTE32, rTE36, rTE40,rTE44, rTE52, rTE56 and rTE60) and C. viscosissima FatB1 (CvB1).

FIG. 9 lists the amino acid (single letter code) present at a givenposition in TE for the indicated organism.

FIG. 10 shows the fatty acid profiles of TE mutants on the right,wherein the green color highlights the major fatty acids produced by theTEs, the cluster analysis of the fatty acid profiles on the left, andthe point mutations in each TE mutant in the middle. The wild-typeenzyme is CvFatB2, which is shown in the color blue. The color orangeindicates residues that have been mutated to the amino acid present atthe corresponding position in CvFatB1. Red points indicate residues thathave been mutated to amino acids that are not present in CvFatB1 orCvFatB2.

DETAILED DESCRIPTION

The present disclosure is predicated, at least in part, on the discoverythat expression of an acyl-acyl carrier protein (ACP) thioesterase (TE)from Bryantella formatexigens (DSM 14469, EET61113.1, ZP_(—)05345975.3,C6LDQ9; Wolin et al., Appl. Environ. Microbiol. 69(10): 6321-6326(October 2003)) in a host cell or organism, such as Escherichia coli,results in an increase in the production of short-chain fatty acids inthe host cell or organism. In this regard, it has been surprisingly andunexpectedly discovered that the introduction of two or more pointmutations in the acyl-ACP TE of B. formatexigens has a synergisticeffect on short-chain activity in the host cell or organism. The presentdisclosure is further predicated on the discovery that the substratespecificity and activity (e.g., total amount of fatty acids produced) ofan acyl-ACP TE, such as a plant acyl-ACP TE, can be affected byintroducing a substrate specificity-altering mutation in the regioncorresponding to amino acids 118-167, such as from about amino acid 118to about amino acid 167, of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The materials and methodshave application for biofuels, industrial lubricants, food oils, and thelike.

In view of the foregoing, a method of increasing production of fattyacids, such as short-chain fatty acids and/or fatty acids having fromabout six to about 12 carbon atoms (C6-C12), such as fatty acids havingfrom about 10 to about 12 carbon atoms (C10-C12), in a host cell ororganism is provided. Thus, the method can be used to increaseproduction of fatty acids having less than about 10 carbon atoms orfatty acids having less than about 12 carbon atoms. The method comprisesintroducing into the host cell or organism and expressing therein anucleic acid molecule comprising a nucleotide sequence encoding anacyl-ACP TE, such as an acyl-ACP TE from FIG. 5, FIG. 9, Table 1, Table2, or www.enzyme.cbirc.iastate.edu (such as family TE14), in particularan acyl-ACP TE from a bacterium, e.g., an acyl-ACP TE from Bryantellaformatexigens. By “short-chain fatty acids” is meant fatty acidscontaining six carbons or less. By “increasing production” is meant anincrease in the production of fatty acids (such as short-chain fattyacids and/or fatty acids having from about six to about 12 carbon atoms,e.g., fatty acids having from about 10 to about 12 carbon atoms, and thelike) such as by at least about 5% (or 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, oreven greater) as compared to the production of fatty acids, such asshort-chain fatty acids and/or fatty acids having from about six toabout 12 carbon atoms, such as fatty acids having from about 10 to about12 carbon atoms, and the like, in the wild-type host organism. Anincrease in the production of one class of fatty acids, such asshort-chain fatty acids and/or fatty acids having from about six toabout 12 carbon atoms, such as fatty acids having from about 10 to about12 carbon atoms, may or may not be reflected in an increase in theoverall production of fatty acids. For example, an increase in theproduction of one class of fatty acids, such as short-chain fatty acids,may be accompanied by a decrease in the production of fatty acids ofother chain lengths, such as medium chain lengths or long chain lengths.In this regard, the introduction into the host cell or organism andexpression therein of a nucleic acid comprising a nucleotide sequenceencoding a different TE, such as one described herein (see, e.g., FIG.5, FIG. 9, Table 1, Table 2, or www.enzyme.cbirc.iastate.edu (e.g.,family TE14)), can result in an increase in the production of fattyacids containing, for example, eight, 10, 12, 14, 16, or more carbons.

Another method of increasing production of fatty acids, such asshort-chain fatty acids and/or fatty acids having from about six toabout 12 carbon atoms (C6-C12), such as fatty acids having from about 10to about 12 carbon atoms (C10-C12), in a host cell or organism is alsoprovided. The method comprises introducing into the host cell ororganism and expressing therein a nucleic acid molecule comprising anucleotide sequence encoding a mutant acyl-ACP TE derived from awild-type acyl-ACP TE, such as an acyl-ACP TE from FIG. 5, FIG. 9, Table1, Table 2, or www.enzyme.cbirc.iastate.edu (e.g., family TE14), inparticular an acyl-ACP TE from a bacterium, e.g., an acyl-ACP TE fromBryantella formatexigens. The mutant acyl-ACP TE produces more fattyacids, such as short-chain fatty acids, in the host cell or organismthan the corresponding wild-type (also referred to as “native”) acyl-ACPTE. “Short-chain fatty acids” and “increasing production” are asdescribed above. Preferably, the mutant acyl-ACP TE derived fromwild-type Bryantella formatexigens acyl-ACP TE differs from wild-typeBryantella formatexigens acyl-ACP TE by two or more amino acid mutationscomprising N169Y and S222I and has increased thioesterase activitycompared to wild-type Bryantella formatexigens acyl-ACP TE.

A method of making a mutant Bryantella formatexigens acyl-ACP TE is alsoprovided. The method comprises making a mutant Bryantella formatexigensacyl-ACP TE comprising two or more amino acid mutations comprising N169Yand S222I. Preferably, and even desirably, the mutant Bryantellaformatexigens acyl-ACP TE has increased thioesterase activity comparedto a corresponding wild-type Bryantella formatexigens acyl-ACP TE.Mutant acyl-ACP TEs can be derived from such wild-type acyl-ACP TEs inaccordance with methods known in the art and exemplified herein.

Also provided is a method of making a chimeric Cuphea viscosissimaacyl-ACP TE. Any suitable method of making a chimera as known in the artand exemplified herein can be used. The method can comprise replacing asegment of a wild-type Cuphea viscosissima acyl-ACP TE with a segment ofanother acyl-ACP TE. Examples of wild-type Cuphea viscosissima acyl-ACPTEs include those encoded by the FatB1 gene (designated CvFatB1) and theFatB2 gene (designated CvFatB2). Any suitable acyl-ACP TE (see, e.g.,FIG. 5, FIG. 9, Table 1, Table 2, and www.enzyme.cbirc.iastate.edu(e.g., family TE14), which website is hereby incorporated by referencefor its teachings regarding acyl-ACP TEs) can serve as the source of thesegment that is used to replace the segment of the wild-type Cupheaviscosissima acyl-ACP TE. Preferably, the acyl-ACP TE gene is anotherCuphea viscosissima acyl-ACP TE. The method can, and preferably does,comprise replacing a segment of the CvFatB1 gene with a segment ofanother acyl-ACP TE gene to produce a chimeric CvFatB1 gene or replacinga segment of a CvFatB2 gene with a segment of another acyl-ACP TE geneto produce a chimeric CvFatB2 gene. In this regard, the method cancomprise replacing a segment of a wild-type CvFatB1 gene with a segmentof a CvFatB2 gene or replacing a segment of a wild-type CvFatB2 genewith a segment of a CvFatB1 gene. Preferably, and even desirably, thechimeric Cuphea viscosissima acyl-ACP TE encodes a chimeric acyl-ACP TE,which (i) has a substrate specificity that differs from thecorresponding wild-type Cuphea viscosissima acyl-ACP TE, (ii) produces atotal amount of fatty acids that differs from the total amount of fattyacids produced by the corresponding wild-type Cuphea viscosissimaacyl-ACP TE, or (iii) has a substrate specificity and produces a totalamount of fatty acids, both of which differ from the correspondingwild-type Cuphea viscosissima acyl-ACP TE. For example, substratespecificity can be changed from a broad-range specificity, a C8specificity, or a C14/C16 specificity to one of the others or aspecificity for a different chain length, such as C4, C6, C8, C10, C12,C14, or C16 (see, e.g., FIG. 5 and Table 2). A difference in substratespecificity can result in the production of a fatty acid not produced bythe wild-type TE or the absence of production of a fatty acid producedby the wild-type TE. Activity levels by the chimeric TE, such as thetotal amount of fatty acids produced, can be increased or decreasedcompared to activity levels by the corresponding wild-type TE.Preferably, activity levels are increased.

TABLE 1 Acyl-ACP TEs Organism GenBank ID No. Ref Seq Uni Prot BACTERIAAcetivibrio cellulolyticus CD2 ZP_09465585.1 Acetobacterium woodii(strain ATCC AFA47597.1 YP_005268486.1 H6LB45 29683/DSM 1030/JCM2381/KCTC 1655) Akkermansia muciniphila (strain ATCC ACD05543.1YP_001878324.1 B2UMI7 BAA-835) Alistipes finegoldii DSM 17242 AFL79015.1YP_006411700.1 Alistipes shahii WAL 8301 CBK64996.1 D4IPY4 Alistipes sp.HGB5 EFR57355.1 ZP_08514792.1 E4MCC6 Alkaliphilus oremlandii (strainOhlLAs) ABW18441.1 YP_001512437.1 A8MEW2 (Clostridium oremlandii strainOhlLAs) Anaeromyxobacter dehalogenans ACL67544.1 YP_002494610.1 B8JAP5(strain 2CP-1/ATCC BAA-258) Anaeromyxobacter sp. (strain Fw109-5)ABS24558.1 YP_001377542.1 A7H762 Anaeromyxobacter sp. (strain K)ACG75405.1 YP_002136534.1 B4UHZ1 Anaerophaga sp. HS1 ZP_09483366.1Anaerophaga thermohalophila DSM ZP_08844891.1 12881 Anaerostipes sp.3_2_56FAA EFV23220.1 ZP_07930626.1 E5VSK1 Arcobacter nitrofigilis(strain ATCC ADG93695.1 YP_003656202.1 D5V083 33309/DSM 7299/LMG7604/NCTC 12251/CI) (Campylobacter nitrofigilis) Arcobacter sp. L.BAK73293.1 YP_005553610.1 G2HVZ0 Atopobium parvulum (strain ATCCACV51065.1 YP_003159656.1 C8WAC7 33793/DSM 20469/JCM 10300/VPI 0546)(Streptococcus parvulus) (Peptostreptococcus parvulus) Bacilluscoagulans (strain 2-6) AEH52240.1 YP_004567626.1 F7Z1I0 Bacteroidesclarus YIT 12056 EGF49737.1 ZP_08298226.1 F3PL79 Bacteroides coprosuisDSM 18011 EGJ70302.1 ZP_08457284.1 F3ZP75 Bacteroides dorei 5_1_36/D4EEB23554.1 ZP_03302607.1 B6W3R2 EEO44480.1 ZP_08794675.1 C3R613Bacteroides eggerthii 1_2_48FAA EFV30016.1 ZP_07934757.1 E5WYK7Bacteroides faecis MAJ27 ZP_09861604.1 Bacteroides fluxus YIT 12057EGF58556.1 ZP_08299596.1 F3PR15 Bacteroides fragilis (strain YCH46)BAD50502.1 YP_101036.1 Q64PS9 Bacteroides fragilis 3_1_12 EFR55122.1ZP_07811188.1 E4W011 Bacteroides helcogenes (strain ATCC ADV45243.1YP_004162829.1 E6ST39 35417/DSM/20613/JCM 6297/P 36- 108) Bacteroidesovatus SD CC 2a EFF59010.1 ZP_06721668.1 D4WRN0 Bacteroides salanitronis(strain DSM ADY35429.1 YP_004257902.1 F0R2N4 18170/JCM 13567/BL78)Bacteroides sp. 1_1_14 EFI05067.1 ZP_06994617.1 D7IBR2 Bacteroides sp.20_3 EEY82391.1 ZP_05286609.1 D0TGY7 EFK61224.1 ZP_06076697.1 E1YZ05ZP_07217422.1 Bacteroides sp. 3_1_19 EFI08712.1 ZP_06985974.1 D7IRY5Bacteroides sp. 3_1_23 EEO56440.1 ZP_04550578.1 C3QWV6 EFI38044.1ZP_07041038.1 D7K661 Bacteroides sp. 3_1_33FAA EEO60747.1 ZP_04541663.1C3PZJ8 EEZ23120.1 ZP_06086837.1 D1JYR1 Bacteroides sp. 3_1_40AEET16328.1 ZP_07997247.1 C6Z619 EFV66622.1 ZP_08799591.1 E5UVX5Bacteroides sp. 4_1_36 EFV26096.1 ZP_07938734.1 E5VAR7 Bacteroides sp.D22 EEO50828.1 ZP_06083560.1 C3QFU4 EEZ04805.1 ZP_06997928.1 D0TQX4EFI15679.1 ZP_08787276.1 D7IYC1 Bacteroides thetaiotaomicron (strainAAO77182.1 NP_810988.1 Q8A611 ATCC 29148/DSM 2079/NCTC10582/E50/VPI-5482) Bacteroides vulgates (strain ATCC ABR40214.1YP_001299836.1 A6L3F0 8482/DSM 1447/NCTC 11154) EFG15793.1 ZP_06744316.1D4VE79 Bacteroides xylanisolvens SD CC 1b. EFG15675.1 ZP_06764643.1D4VEU2 Bacteorides xylanisolvens XB1A CBK66370.1 D6D8M5 Bilophilawadsworthia 3_1_6 EFV45711.1 ZP_07943134.1 E5Y2P2 butyrate-producingbacterium SS3/4 CBL41593.1 D7GUV1 butyrate-producing bacterium SSC/2CBL38064.1 D4MZL9 Butyrivibrio crossotus DSM 2876 EFF67558.1ZP_05793158.1 D4S2V3 Butyrivibrio fibrisolvens CBK73219.1 D4IZD0Butyrivibrio proteoclasticus (strain ADL35342.1 YP_003831924.1 E0RY84ATCC 51982/DSM 14932/B316) Clostridium proteoclasticum) Calditerrivibrionitroreducens (strain ADR19107.1 YP_004051270.1 E4TIX5 DSM 19672/NBRC101217/Yu37-1) Caldithrix abyssi DSM 13497 EHO418883.1 ZP_09550215.1H1XX98 Capnocytophaga gingivalis ATCC EEK15190.1 ZP_04057029.1 C2M39333624 Capnocytophaga ochracea (strain ACU91765.1 YP_003140326.1 C7M565ATCC 27872/DSM 7271/JCM 12966/ VPI 2845) (Bacteroides ochraceus)Capnocytophaga ochracea F0287 EFS97621.1 ZP_07866279.1 E4MRT3Capnocytophaga sp. oral taxon 329 str. EGJ52443.1 ZP_08450270.1 F3Y4U4F0087 Capnocytophaga sp. oral taxon 329 str. EGJ54408.1 ZP_08448171.1F3XZ88 F0087 Capnocytophaga sp. oral taxon 338 str. EGD34946.1ZP_08201032.1 F0IDA8 F0234 Capnocytophaga sputigena ATCC EEB66819.1ZP_03389980.1 E2MZN9 33612 Carnobacterium maltaromaticum ZP_10276496.1ATCC 35586 Carnobacterium sp. (strain 17-4) AEB30554.1 YP_004375570.1F4BN85 Cellulosilyticum lentocellum (strain ADZ85723.1 YP_004310921.1F2JL78 ATCC 49066/DSM 5427/NCIMB 11756/RHM5) (Clostridum lentocellum)Cellulosilyticum lentocellum (strain ADZ84608.1 YP_004309806.1 F2JLT2ATCC 49066/DSM 5427/NCIMB 11756/RHM5) (Clostridium lentocellum)Clostridium acetobutylicum (strain AAK81514.1 NP_350174.1 F0KBI3 ATCC824/DSM 792/JCM 1419/LMG ADZ22635.1 YP_004638245.1 F7ZTD9 5710/VKMB-1787) AEI32944.1 YP_005672730.1 Q97D89 Clostridium beijerinckii(strain ATCC ABR37178.1 YP_001312134.1 A6M3J8 51743/NCIMB 8052)(Clostridium acetobutylicum) Clostridium beijerinckii (strain ATCCABR32877.1 YP_001307833.1 A6LR97 51743/NCIMB 8052) (Clostridiumacetobutylicum) Clostridium botulinum (strain 657/Type ACQ55199.1YP_002864623.1 B1QMJ6 Ba4) EDT85214.1 ZP_02618356.1 C3KWG6 Clostridiumbotulinum (strain Alaska ACD52320.1 YP_001922691.1 B2V1S4 E43/Type E3)Clostridium botulinum (strain ATCC ABS34504.1 YP_001256092.1 A5I7Y719397/Type A) ABS37570.1 YP_001385928.1 A7FZF7 CAL85172.1 YP_001389335.1Clostridium botulinum (strain Eklund ACD25059.1 YP_001887708.1 B2TRE217B/Type B) Clostridium botulinum (strain H04402 ABS42332.1YP_001392970.1 A7GJL0 065/Type A5) ACA45501.1 YP_001783249.1 B1IHP0ADG01324.1 YP_005676524.1 D5VZ84 CBZ05511.1 YP_005680239.1 E8ZRC8Clostridium botulinum (strain ACO86035.1 YP_002806157.1 B1QFF4Kyoto/Type A2) EDT80125.1 ZP_02615745.1 C1FNL6 Clostridium botulinum(strain Loch ACA57020.1 YP_001788956.1 B1KU83 Maree/Type A3 Clostridiumbotulinum BKT015925 AEB74722.1 YP_004394719.1 F4A6R7 Clostridiumbotulinum C str. Eklund EDS76894.1 ZP_02621951.1 B1BC83 Clostridiumbotulinum C str. Stockholm EGO89051.1 F7MJC2 Clostridium botulinum Dstr. 1873 EES92019.1 ZP_04862128.1 C5VPS2 Clostridium botulinum E1 str.‘BoNT E EES49023.1 ZP_04821738.1 C5UVX9 Beluga’ Clostridium butyricum E4str. BoNT E EDT76365.1 ZP_02948643.1 B1QU73 BL5262 EEP52456.1ZP_04529638.1 C4IMU3 Clostridium carboxidivorans P7 EET84629.1ZP_05394929.1 C6Q1L2 EFG87972.1 ZP_06855226.1 Clostridium cellulolyticum(strain ACL76790.1 YP_002506770.1 B8I625 ATCC 35319/DSM 5812/JCM6584/H10) Clostridium cellulovorans (strain ADL54009.1 YP_003845773.1D9SPA7 ATCC 35296/DSM 3052/OCM ZP_07630281.1 3/743B) Clostridiumhahtewayi DSM 13479 EFC97397.1 ZP_06116072.2 D3ALA6 Clostridium novyi(strain NT) ABK60402.1 YP_877012.1 A0PXB0 Clostridium papyrosolvens DSM2782 EGD46508.1 ZP_08194021.1 F1TGE3 Clostridium perfringens (strainATCC ABG82470.1 YP_697308.1 Q0TM32 13124/NCTC 8237/Type A) Clostridiumperfringens (strain ATCC ABG83514.1 YP_697307.1 B1BYH2 13124/NCTC8237/Type A) EDT13255.1 ZP_02634160.1 B1R6C7 EDT24316.1 ZP_02635484.1Q0TM33 Clostridium perfringens (strain ABG85584.1 YP_699873.1 Q0SPT4SM101/Type A) Clostridium perfringens CPE str. F4969 EDT25816.1ZP_02640550.1 B1RJP3 Clostridium perfringens CPE str. F4969 EDT25796.1ZP_02640551.1 B1RJP4 Clostridium perfringens F262 EIA15751.1 H7CZX6Clostridium perfringens F262 EDS81696.1 ZP_02643956.1 B1BEU6 EDT77142.1ZP_02863338.1 B1RTS9 EIA15750.1 H7CZX5 Clostridium phytofermentans(strain ABX40638.1 YP_001557377.1 A9KS07 ATCC 700394/DSM 18823/ISDg)Clostridium saccharolyticum (strain ADL03414.1 YP_003821037.1 D9R5Y0ATCC 35040/DSM 2544/NRCC 2533 WM1) Clostridium saccharolyticumCBK77093.1 D6DHB9 Clostridium sp. 7_2_43FAA EEH99678.1 ZP_05132784.1C1IBG7 Clostridium sp. 7_2_43FAA EEH97843.1 ZP_05130949.1 C1I6P2Clostridium sp. BNL1100 AEY65028.1 YP_005146833.1 H2JCC1 Clostridium sp.DL-VIII EHI96936.1 ZP_09202343.1 G7MBI0 Clostridium sp. M62/1 EFE13917.1ZP_06345069.2 D4C8T0 Clostridium sporogenes PA 3679 EHN13726.1 G9F4F0Clostridium tetani (strain AAO34771.1 NP_780834.1 Q899Q1Massachusetts/E88) Clostridium thermocellum (strain DSM ABN54268.1YP_001039461.1 A3DJY9 1313/LMG 6656/LQ8) ADU73702.1 YP_005687153.1C7HJ46 EEU00270.1 ZP_05430844.1 D1NHY5 EFB38222.1 ZP_06247582.1 E6UU77EIC03340.1 H8EG82 EIC10345.1 H8ERY8 Coprococcus catus GD/7 CBK80368.1D4J7P7 Coprococcus sp. ART55/1 CBK82356.1 D5HHV1 Cryptobacterium curtum(strain ATCC ACU95033.1 YP_003151715.1 C7ML86 700683/DSM 15641/12-3)Deferribacter desulfuricans (strain BAI79538.1 YP_003495294.1 D3PAB5 DSM14783/JCM 11476/NBRC 101012/SSM1) Denitrovibrio acetiphilus (strain DSMADD68769.1 YP_003504725.1 D4H1K9 12809/N2460) Desulfatibacillumalkenivorans (strain ACL04336.1 YP_002431804.1 B8FIU5 AK-01)Desulfitobacterium dehalgenans ATCC AFM00949.1 YP_006430742.1 51507Desulfitobacterium hafniense (strain ACL21191.1 YP_002459627.1 B8G1D8DCB-2/DSM 10664) Desulfitobacterium metallireducens EHC09806.1ZP_08979048.1 G6GL79 DSM 15288 Desulfobacterium autotrophicum ACN14977.1YP_002603141.1 C0QBW5 (strain ATCC 49314/DSM 3382/HRM2) Desulfococcusoleovorans (strain DSM ABW68393.1 YP_001530470.1 A8ZWR2 6200/Hxd3)Desulfohalobium retbaense (strain ACV69537.1 YP_003199115.1 C8X540 DSM5692) Desulfomicrobium baculatum (strain ACU90117.1 YP_003158533.1C7LNE8 DSM 4028/VKM B-1378) Desulfovibrio baculatus) Desulfonatronospirathiodismutans EFI34439.1 ZP_07016503.1 D6SNW3 ASO3-1 Desulfosporosinusmeridiei DSM EHC14266.1 ZP_08981281.1 G6G6K3 13257 Desulfosporosinusorientis (strain AET66411.1 YP_004968926.1 G7W7Y5 ATCC 19365/DSM765/NCIMB 8382/VKM B-1628) (Desulfotomaculum orientis) Desulfosporosinusyoungiae DSM EHQ87820.1 ZP_09652397.1 H5Y1R7 17734 Desulfotomaculumcarboxydivorans AEF93400.1 YP_004496312.1 F6B7F0 (strain DSM 14880/VKMB-2319/CO- 1-SRB) Desulfotomaculum nigrificans DSM EGB20954.1ZP_08115620.1 F0DQC6 574 Desulfovibrio aespoeensis (strain ADU63859.1YP_004122605.1 E6VY45 ATCC 700646/DSM 10631/Aspo-2) Desulfovibrioafricanus str. Walvis Bay EGJ50649.1 YP_005052308.1 F3YXU7 Desulfovibriodesulfuricans (strain ABB38135.2 YP_387830.2 Q312L1 G20) Desulfovibriodesulfuricans ND132 EGB14659.1 YP_005167463.1 F0JE50 Desulfovibriosalexigens (strain ATCC ACS79414.1 YP_002990953.1 C6BRH4 14822/DSM2638/NCIB 8403/VKM B- 1763) Desulfovibrio sp. A2 EGY25981.1ZP_08865364.1 G2H7B6 Desulfovibrio vulgaris (strain Miyazaki ACL08376.1YP_002435844.1 B8DRT9 F/DSM 19637) Dethiosulfovibrio peptidovorans DSMEFC90467.1 ZP_06391526.1 D2Z4D8 11002 Elusimicrobium minutum (strainACC98705.1 YP_001876042.1 B2KDV9 Pei191) Enterococcus casseliflavus ATCCEGC68270.1 ZP_08147098.1 F0EPP5 12755 Enterococcus casseliflavus EC10EEV28127.1 ZP_05644794.1 C9ATN7 EEV34451.1 ZP_05651118.1 C9CHB4Enterococcus casseliflavus EC20 EEV37743.1 ZP_05654410.1 C9A551Enterococcus faecalis (strain 62) ADX78961.1 YP_005704694.1 C7CPH3EET94418.1 ZP_05421510.1 C7U457 EEU22239.1 ZP_05501873.1 C7UJZ9EEU64872.1 ZP_05561915.1 C7USW8 EEU70266.1 ZP_05567309.1 C7V886EEU75370.1 ZP_05574399.1 C7VHP9 EEU76113.1 ZP_05575142.1 C7VYJ9EEU81059.1 ZP_05580088.1 C7WCN3 EEU84199.1 ZP_05583228.1 C7WH64EEU86888.1 ZP_05592094.1 C7WSC9 EEU92436.1 ZP_05597642.1 D4V053EFG20655.1 ZP_06745965.1 F0PFE4 Enterococcus faecalis (strain ATCCAEA92939.1 YP_005707309.1 F2MNV7 47077/OG1RF) Enterococcus faecalis ATCC29200 EEN72504.1 ZP_04437017.1 C2H016 Enterococcus faecalis DAPTO 512EFE15755.1 ZP_06630131.1 D4EIL1 EFE20531.1 ZP_06631594.1 D4EX30EFQ10983.1 ZP_07765336.1 E2YB09 EFQ68629.1 ZP_07768525.1 E2YJM4Enterococcus faecalis Merz96 EEU66704.1 ZP_05563747.1 C7VQU1 EEU78784.1ZP_05577813.1 C7WV73 Enterococcus faecalis T11 EEU89934.1 ZP_05595140.1C7V0W5 Enterococcus faecalis T2 EET97613.1 ZP_05424705.1 C7CYL8Enterococcus faecalis T8 EEU15993.1 ZP_05475136.1 C7UCD7 EEU27232.1ZP_05557722.1 C7Y8I5 Enterococcus faecalis TUSoD Ef11 EFK76243.1ZP_07108041.1 E1EUM8 Enterococcus faecalis TX0012 EFT94231.1 E6I3I6Enterococcus faecalis TX0104 EEI11131.1 ZP_03949391.1 C0X740Enterococcus faecalis TX0309B EFU87020.1 E6GSL8 EFU94467.1 E6H424Enterococcus faecalis TX1467 EFM69547.1 ZP_07551346.1 E0G5A0 EFM72961.1ZP_07553437.1 E0GB90 EFM80076.1 ZP_07562578.1 E0GWQ0 EFM82210.1ZP_07568717.1 E0H6A2 EFQ13284.1 ZP_07759854.1 E2Y3Z3 EFQ15104.1ZP_07764076.1 E2YZ82 EFQ70935.1 ZP_07770885.1 E2Z4S5 EFT38179.1 E6F2Y1EFT44150.1 E6F559 EFT47364.1 E6FHC7 EFT90826.1 E6FQ99 EFT97839.1 E6FWN8EFU00982.1 E6G0U5 EFU02883.1 E6G9N2 EFU05122.1 E6GLN8 EFU10142.1 E6HEB6EFU11766.1 E6HN77 EFU14622.1 E6HUS1 EFU16821.1 E6IDJ0 EFU88613.1 E6IKL5EGG56243.1 F3R4H1 Enterococcus faecalis TX2141 EFT88049.1 E6IVY9Enterococcus faecalis TX4000 EEN73225.1 ZP_04436471.1 C2DIA3 EFM65997.1ZP_07556393.1 E0GJP6 EFM77239.1 ZP_07572356.1 E0HGP1 EFT40437.1 E6ESI6Enterococcus faecium (strain Aus0004) AFC64296.1 YP_005355414.1 C9B6S0EAN09806.1 ZP_00603869.1 C9BR75 EEV42502.1 ZP_05659169.1 C9BZH1EEV46437.1 ZP_05663104.1 C9C309 EEV47997.1 ZP_05664664.1 C9CD36EEV53223.1 ZP_05669890.1 D0AP61 EEV57800.1 ZP_05674467.1 D4QR52EEW62756.1 ZP_05831946.1 D4QYX5 EFF21534.1 ZP_06675770.1 D4RSJ8EFF29090.1 ZP_06676257.1 D4SPZ7 EFF30890.1 ZP_06678973.1 G9SNG7EFF35697.1 ZP_06701551.1 G9SWE6 EHM36206.1 H8L8C1 EHM36898.1 Q3Y000Enterococcus faecium Com15 EEV62230.1 ZP_05678897.1 C9AQE0 Enterococcusfaecium E1636 EEW64692.1 ZP_05923461.1 D0AHZ9 EFD09525.1 ZP_06446970.1D3LH99 EFF23086.1 ZP_06695563.1 D4RAG0 Enterococcus faecium E1679EFF25207.1 ZP_06699424.1 D4RLH1 Enterococcus faecium E980 EFF38835.1ZP_06681449.1 D4QHC6 Enterococcus faecium PC4.1 EEV51369.1 ZP_05668036.1C9AJN9 EEV60229.1 ZP_05676896.1 C9BGE2 EFF61513.1 ZP_06624194.1 D4VWH8Enterococcus faecium TX0133a01 AFK59819.1 YP_006376801.1 E4I8N4EFR68006.1 ZP_07846162.1 E4IJA4 EFR70537.1 ZP_07849882.1 E4INZ4EFR75054.1 ZP_07851522.1 EVIXY0 EFR77028.1 ZP_07854658.1 EVJAY8EFS06349.1 ZP_07859216.1 EVJI68 EFS10037.1 ZP_07861746.1 Enterococcusfaecium TX1330 EEI61496.1 ZP_03980399.1 C2H7W0 Enterococcus gallinarumEG2 EEV32970.1 ZP_05649637.1 C9A053 Enterococcus italicus DSM 15952EFU73343.1 ZP_07896506.1 E6LHJ1 Ethanoligenens harbinense (strainADU28280.1 YP_004093011.1 E6U8G1 DSM 18485/JCM 12961/CGMCC 1.5033YUAN-3) Eubacterium cellulosolvens 6 EIM57815.1 ZP_10167425.1Eubacterium limosum (strain KIST612) ADO35661.1 YP_003958624.1 E3GJ26Eubacterium rectale DSM 17629 CBK89551.1 D6E2B1 Eubacterium rectalM104/1 CBK94159.1 D4JKL2 Eubacterium saburreum DSM 3986 EFU75440.1ZP_07905804.1 E6LS63 Eubacterium siraeum 70/3 CBK97519.1 D4JWQ0Eubacterium siraeum V10Sc8a CBL35446.1 D4MNW3 Faecalibacteriumprausnitzii L2-6 CBK98400.1 D4K4F7 Fibrella aestuarina BUZ 2 CCG99613.1I0K660 Fibrisoma limi BUZ 3 CCH55838.1 Fibrobacter succinogenes (strainACX75214.1 YP_003249696.1 C9RRM8 ATCC 19169/S85) ADL24713.1YP_005822012.1 Finegoldia magna (strain ATCC BAG08537.1 YP_001692427.1B0S2E7 29328) (Peptostreptococcus magnus) Finegoldia magna EFL54101.1ZP_07321135.1 E1KXS7 SY403409CC001050417 EGS34728.1 F9MZ32Flavobacterium columnare (strain AEW86359.1 YP_004942152.1 G8X6Z8 ATCC49512/CIP 103533/TG 44/87) Flavobacterium frigoris PS1 EIA08417.1ZP_09895618.1 H7FRY9 Flavobacterium johnsoniae (Strain ABQ06468.1YP_001195787.1 A5FE97 ATCC 17061/DSM 2064/UW101) Cytophaga johnsonaeFlavonifractor plautii ATCC 29863 EHM53486.1 ZP_09383254.1 G9YNF5Flexistipes sinusarabici (strain DSM AEI14379.1 YP_004602947.1 F8E4264947/MAS 10) Fructobacillus fructosus KCTC 3544 ZP_08660317.1Geobacillus sp. (strain Y412MC10) ACX63219.1 YP_003241026.1 D3EF08Geobacter lovleyi (Strain ATCC BAA- ACD96083.1 YP_001952603.1 B3E5961151/DSM 17278/SZ) Geobacter metallireducens (strain GS- ABB31963.1YP_384688.1 H1L7J4 15/ATCC 53774/DSM 7210) EHP86324.1 Q39UW1 Geobactersp. (strain FRC-32) ACM20973.1 YP_002538074.1 B9M0X0 Granulicatellaadiacens ATCC 49175 EEW37696.1 ZP_05737219.1 C8NEY7 Granulicatellaelegans ATCC 700633 EEW93633.1 ZP_05851687.1 D0BKN0 Haliscomenobacterhydrossis (strain AEE52567.1 YP_004449440.1 F4KWT4 ATCC 27775/DSM1100/LMG 10767 O) Haloplasma contractile SSD-17B EGM25295.1ZP_08557504.1 F7Q2G6 EGM26151.1 ZP_08558128.1 Jonquetella anthropi DSM22815 EHM12447.1 H0ULI2 Jonquetella anthropi E3_33 E1 EEX49185.1ZP_05859848.1 C9M5Q8 Lachnospiraceae bacterium EFV17918.1 ZP_07955084.1E5VG94 5_1_63FAA Lachnospiraceae bacterium oral taxon EHO50163.1ZP_09561948.1 H1LYH8 082 str. F0431 Lactobacillus acidipiscis KCTC 13900ZP_09456326.1 Lactobacillus acidophilus (strain 30SC) ADZ06571.1YP_004286708.1 F0TIR4 Lactobacillus aciophilus (strain ATCC AAV42277.1YP_193308.1 Q5FLZ7 700396/NCK56/N2/NCFM) Lactobacillus acidophilus ATCC4796 EEJ76335.1 ZP_04021090.1 C2HMJ5 Lactobacillus amylolyticus DSM11664 EFG55410.1 ZP_06818559.1 D4YTY9 Lactobacillus amylovorus (strainGRL ADQ58392.1 YP_004031187.1 E4SLD4 1118) AEA31360.1 YP_005853365.1F2M221 Lactobacillus animalis KCTC 3501 ZP_08549496.1 Lactobacillusbrevis (strain ATCC ABJ63754.1 YP_794785.1 Q03SR8 367/JCM 1170)Lactobacillus brevis subsp. gravesensis EEI69866.1 ZP_03940727.1 C2D5L9ATCC 27305 Lactobacillus buchneri (strain NRRL AEB73621.1 YP_004398684.1F4FX93 B-30929) Lactabacillus buchneri ATCC 11577 EEI18325.1ZP_03943743.1 C0WUL3 Lactobacillus casei (strain ATCC 334) ABJ70998.1YP_003789283.1 D8GB52 ADK19433.1 YP_005857330.1 F2MA80 AEA54746.1YP_005860469.1 F2MJ21 AEA57928.1 YP_807440.1 Q035X4 Lactobacilluscoleohominis 101-4-CHN EEU30164.1 ZP_05553571.1 C7XWA4 Lactobacilluscrispatus (strain ST1) CBL49834.1 YP_003600859.1 D5H1E9 Lactobacilluscrispatus 125-2-CHN EEU18812.1 ZP_05550017.1 C7XLF9 Lactobacilluscrispatus CTV-05 EEJ70241.1 ZP_03995680.1 C2KCV6 EEX28703.1ZP_06020517.1 D0DJR2 EFE00376.1 ZP_06626062.1 D4FBS4 EFQ44288.1ZP_07789659.1 E3R4N0 Lactobacillus crispatus MV-1A-US EEU28844.1ZP_05554513.1 C7Y3T1 Lactobacillus delbrueckii subsp. ADY85572.1YP_005852596.1 F0JZ70 bulgaricus (strain 2038) Lactobacillus delbrueckiisubsp. ABJ58999.1 YP_813437.1 Q048X3 bulgaricus (strain ATCC BAA-365)Lactobacillus delbrueckii subsp. ADQ61561.1 YP_004034538.1 E4SWA3bulgaricus (strain ND02) Lactobacillus delbrueckii subsp. EFK32863.1ZP_07091661.1 D8FL81 bulgaricus PB2003/044-T3-4 Lactobacillusdelbrueckii subsp. lactis EGD27772.1 F0HUG7 DSM 20072 Lactobacillusfarciminis KCTC 3681 ZP_08576095.1 Lactobacillus fermentum (strain CECTADJ40858.1 YP_005848352.1 D8IGS7 5716) Lactobacillus fructivorans KCTC3543 ZP_08652157.1 Lactobacillus gasseri (strain ATCC ABJ59782.1YP_814220.1 Q045U0 33323/DSM 20243) Lactobacillus gasseri 202-4EEQ26038.1 ZP_04643995.1 C4VSR8 Lactobacillus gasseri 224-1 EFB62115.1ZP_06262095.1 D1YK76 Lactobacillus gasseri JV-V03 EFJ69165.1ZP_07058478.1 D7V535 Lactobacillus gastricus PS3 EHS87218.1ZP_09786106.1 H4GIM3 Lactobacillus helveticus (strain H10) ADX69593.1YP_005849580.1 F0NV99 Lactobacillus helveticus MTCC 5463 EEW67886.1ZP_05752683.1 C9M2C2 EGF34731.1 F3MQC6 Lactobacillus hilgardii ATCC 8290EEI25650.1 ZP_03952565.1 C0XG64 Lactobacillus iners AB-1 ZP-07267176.1Lactobacillus iners ATCC 55195 EEW51705.1 ZP_05744259.1 C8PCP7EFO66686.1 ZP_07697641.1 E1NFD0 EFQ50621.1 ZP_07732239.1 E3BYM9EFU79110.1 ZP_07906033.1 E6LSU2 Lactobacillus iners LactinV 09V1-cEFO67514.1 ZP_07699507.1 E1NKQ9 Lactobacillus iners LEAF 3008A-aEFQ51957.1 ZP_07731033.1 E3C233 Lactobacillus iners SPIN 1401GEFO69137.1 ZP_07700645.1 E1NP18 EGG31776.1 ZP_08277548.1 F3M0Y4Lactobacillus iners SPIN 2503V10-D EFO71603.1 ZP_07703903.1 E1NYD0Lactobacillus iners UPII 143-D EFQ47178.1 ZP_07733650.1 E3BU75EFQ49253.1 ZP_07735732.1 E3BVE7 EGC79722.1 ZP_08173986.1 F0GLZ3Lactobacillus iners UPII 60-B EGC80907.1 ZP_08175329.1 F0GQU0Lactobacillus jensenii 208-1 EEQ24340.1 ZP_04645666.1 C4VMZ1 EEX27386.1ZP_05865781.1 D0DNZ9 EFA93633.1 ZP_06339831.1 D1WHH0 Lactobacillusjohnsonii DPC 6026 AEB92746.1 YP_005861696.1 F4AEU9 Lactobacillusjohnsonii pf01 EGP13921.1 F7SCN1 Lactobacillus kefiranofaciens (strainAEG39778.1 YP_004561880.1 F6CD69 ZW3) Lactobacillus kisonensis F0435EHO52285.1 ZP_09555400.1 H1LET0 Lactobacillus malefermentans KCTCZP_09441303.1 3548 Lactobacillus mali KCTC 3596 = DSM ZP_09447064.120444 Lactobacillus mucosae LM1 EHT15844.1 ZP_09815086.1 H3RQN4Lactobacillus oris F0423 EGS36091.1 F9JK82 Lactobacillus oris PB013-T2-3EFQ53035.1 ZP_07729836.1 E3C864 Lactobacillus paracasei subsp.EEI68786.1 ZP_03963784.1 C2FBR3 paracasei 8700:2 EEQ66724.1ZP_04673142.1 C5F8Y0 Lactobacillus parafarraginis F0439 EHL96655.1ZP_09393527.1 G9ZRF4 Lactobacillus plantarum (strain ATCC ADN97761.1YP_003923855.1 D7VG69 BAA-793/NCIMB 8826/WCFS1) CCC78182.1YP_004888696.1 E1TKY4 EFK27869.1 ZP_07079657.1 F9ULU3 EHS83236.1 H3P172Lactobacillus reuteri (strain ATCC AEI57752.1 YP_004650042.1 C2GRC855730/SD2112) EEI64955.1 ZP_03975201.1 F8DLS3 Lactobacillus reuteri100-23 EDX41870.1 ZP_03074105.1 B3XQR9 Lactobacillus rhamnosus (strainATCC BAI42696.1 YP_003172003.1 B5QQB5 53103/GG) CAR88152.1YP_005866661.1 C7TEV9 EDY98171.1 ZP_03212443.1 G6AK63 EHJ21134.1 G6JOH2EHJ36340.1 Lactobacillus rhamnosus (strain Lc AER64996.1 YP_003174934.1C2JZ75 705) CAR91083.1 YP_005873849.1 C7TLJ9 EEN79670.1 ZP_04441678.1G7UXI5 Lactobacillus ruminis (strain ATCC AEN77890.1 YP_004831826.1G2SMB8 27782/RF3) Lactobacillus ruminis SPM0211 EFZ34938.1 ZP_08080403.1E7FPK7 EGM50173.1 ZP_08564070.1 F7R2D3 EGX99156.1 Lactobacillussalivarius (strain CECT ADJ79282.1 YP_005864069.1 D8ILY0 5713)Lactobacillus salivarius (strain ABE00028.1 YP_536111.1 C2EGC7 UCC118)EEJ74495.1 ZP_04009005.1 Q1WSV1 Lactobacillus salivarius ACS-116-V-EFK79641.1 ZP_07206660.1 E1JN74 Col5a Lactobacillus salvarius GJ-24EGL99750.1 F5VCC4 EGM52363.1 F7QU96 Lactobacillus salivarius SMXD51EIA32146.1 H7G0I9 Lactobacillus vaginalis ATCC 49540 EEJ40900.1ZP_03959573.1 C2ETB7 Lactobacillus versmoldensis KCTC ZP_09443147.1 3814Lactobacillus zeae KCTC 3804 ZP_09454130.1 Lactococcus garvieae IPLA31405 EIT66252.1 Lactococcus garvieae (strain Lg2) BAK58395.1YP_004779059.1 F9V8F4 (Enterococcus seriolicida) BAK60363.1YP_005870647.1 F9VDG2 Lactococcus lactis subsp. cremoris ABJ72781.1YP_809203.1 Q02Z41 (strain SK11) Lactococcus lactis subsp. cremoris A76AEU40439.1 YP_005875862.1 G8P2V5 Lactococcus lactis subsp. lactis(strain ADZ63759.1 YP_005868493.1 F2HJJ6 CV56) EHE92562.1 G6FES7Lactococcus lactis subsp. lactis IO-1 BAL51042.1 H5SYX8 Leuconostoccitreum (strain KM20) ACA83334.1 YP_001728778.1 B1MVT0 CCF27846.1 H1WZU7Leuconostoc citreum LBAE C10 CCF23736.1 H1WN37 Leuconostoc citreum LBAEC11 CCF26033.1 H1WUN4 Leuconostoc fallax KCTC 3537 ZP_08313133.1Leuconostoc mesenteroides subsp. ABJ61410.1 YP_005173661.1 G7VJW8mesenteroides (strain ATCC AET29695.1 YP_817783.1 Q03ZG2 8293/NCDO 523)Leuconostoc pseudomesenteroides ZP_08658910.1 KCTC 3652 Leuconostocpseudomesenteroides ZP_08657880.1 KCTC 3652 Marvinbryantia formatexigensDSM EET58368.1 ZP_05348824.1 C6LLV8 14469 Melissococcus plutonius(strain ATCC BAK22205.1 YP_004457014.1 F3YCH7 35311/CIP 104052/LMG20360/NCIMB 702443) Melissococcus plutonius (strain BAL61565.1YP_005319060.1 H5T322 DAT561) Mesotoga prima MesG1.Ag.4.2 AFK07784.1YP_006347027.1 Microscilla marina ATCC 23134 EAY28464.1 ZP_01690629.1A1ZMT4 Moorella thermoacetica (strain ATCC ABC20493.1 YP_431036.1 Q2RGE639073) Myroides odoratus DSM 2801 EHQ43781.1 ZP_09673466.1 H1ZDF8Odoribacter splanchnicus (strain ADY34476.1 YP_004254656.1 F9ZBU7 ATCC29572/DSM 20712/JCM 15291/ NCTC 10825/1651/6) (Bacteroides splanchnicus)Oenococcus kitaharae DSM 17330 EHN59872.1 G9WGP5 Olsenella uli (strainATCC 49627/DSM ADK67921.1 YP_003800801.1 E1QZV7 7084/CIP 109912/JCM12494/VPI D76D-27C) (Lactobacillus uli) Opitutus terrae (strain DSMACB75273.1 YP_001817873.1 B1ZXQ1 11246/PB90-1) Ornithinibacillusscapharcae TW25 ZP_08784004.1 Paenibacillus dendritiformis C454EHQ61755.1 ZP_09676931.1 H3SGM0 Paenibacillus lactis 154 EHB50198.1ZP_09004493.1 G4HNN3 Paenibacillus sp. HGF5 EGG35794.1 ZP_08280757.1F3MA61 Paenibacillus vortex V453 EFU42569.1 ZP_07898346.1 E5YSB9Paludibacter propionicigenes (strain ADQ78301.1 YP_004041286.1 E4T0E2DSM 17365/JCM 13257/WB4) Parabacteroides distasonis (strain ABR43801.1YP_001303423.1 A6LDN7 ATCC 8503/DSM 20701/NCTC 11152) Parabacteroidessp. D13 EEU50458.1 ZP_05546795.1 C7XCA8 Paraprevotella clara YIT 11840EHH00544.1 ZP_09107765.1 G5SQZ1 Paraprevotella xylaniphila YIT 11841EGG54116.1 ZP_08320615.1 F3QU31 Pediococcus acidilactici DSM 20284EFL95888.1 ZP_07367805.1 E0NFJ4 Pediococcus acidilactici MA18/5MEFA26407.1 ZP_06197399.1 D2EKP7 EHJ20298.1 G6IS05 Pediococcuspentosaceus (strain ATCC ABJ68507.1 YP_804949.1 H8G000 25745/183-1w)CCG89967.1 Q03E65 Pelobacter propionicus (strain DSM ABL00830.1YP_902887.1 A1AU09 2379) Peptoniphilus harei ACS-146-V-Sch2b EFR32523.1ZP_07822609.1 E4L0C9 Prevotella bivia JCVIHMP010 EFB92152.1ZP_06269388.1 D1Y0N5 EIM31835.1 Prevotella buccae ATCC 33574 EFU30435.1ZP_07882963.1 E6K8D5 Prevotella buccalis ATCC 35310 EFA92524.1ZP_06286413.1 D1W477 Prevotella dentalis DSM 3688 EGQ16303.1ZP_08669671.1 F9D1E1 Prevotella dentalis DSM 3688 EHO56109.1 H1MBA2Prevotella denticola (strain F0289) AEA20475.1 YP_004329120.1 F2KTP5Prevotella denticola CRIS 18C-A EGC84969.1 ZP_08173659.1 F0HB58Prevotella disiens FB035-09AN EFL45598.1 ZP_07323756.1 E1KSA6 Prevotellaintermedia 17 AFJ08475.1 YP_006299246.1 Prevotela marshii DSM 16973EFM02212.1 ZP_07365421.1 E0NRS4 Prevotella melaninogenica (strainADK95990.1 YP_003814035.1 D9RUL0 ATCC 25845/DSM 7089/JCM 6325/VPI2381/B282) (Bacteroides melaninogenicus) Prevotella multiformis DSM16608 EGC20653.1 ZP_08135691.1 F0F5N4 Prevotella multisaccharivorax DSMEGN58078.1 ZP_08580508.1 F8NCP3 17128 Prevotella nigrescens ATCC 33563EGQ15946.1 ZP_08672539.1 F9D9K9 Prevotella oralis ATCC 33269 EFZ37525.1ZP_08084447.1 E7RP82 Prevotella oris C735 EFI48008.1 ZP_07035544.1D7NEM6 Prevotella ruminicola (strain ATCC ADE82257.1 YP_003574402.1D5ERZ8 19189/JCM 8958/23) Prevotella salivae DSM 15606 EFV04584.1ZP_07961907.1 E6MNZ7 Prevotella sp. oral taxon 306 str. F0472 EID32261.1ZP_09968086.1 I0T9F8 Prevotella stercorea DSM 18206 EHJ38668.1ZP_09198687.1 G6AZ54 Pseudoramibacter alactolyticus ATCC EFV02259.1ZP_07920643.1 E6MF99 23263 Rhodothermus marinus (strain ATCC ACY48916.1YP_003291304.1 D0MKK4 43812/DSM 4252/R-10) Rhodothermus obamensis)Rhodothermus marinus SG0.5JP17-172 AEN72763.1 YP_004824600.1 G2SK07Roseburia hominis (strain DSM AEN95631.1 YP_004837563.1 G2T1Y716839/NCIMB 14029/A2-183) Roseburia intestinalis L1-82 EEV02992.1ZP_04741938.1 C7G5B5 Roseburia intestinalis XB6B4 CBL09912.1 D4KSR0CBL12214.1 D4KXX4 Ruminococcus albus (strain ATCC ADU24217.1YP_004090103.1 E6UKM1 27210/DSM 20455/JCM 14654/NCDO 2250/7)Ruminococcus obeum A2-162 CBL24676.1 D4LV68 Ruminococcus sp. SR1/5CBL20901.1 D4LM40 Ruminococcus torques L2-14 CBL26041.1 D4M479Salinibacter ruber (strain DSM ABC43900.1 YP_444210.1 Q2S6H1 13855/M31)Salinibacter ruber (strain M8) CBH22976.1 YP_003569928.1 D5H4M1Sphaerochaeta pleomorpha (strain AEV29849.1 YP_005062859.1 G8QR01 ATCCBAA-1885/DSM 22778/Grapes) Sphingobacterium spiritovorum ATCC EEI90316.1ZP_03970072.1 C2G3W1 33300 Sphingobacterium spiritivorum ATCC EFK55869.1ZP_07082740.1 D7VQ18 33861 Spirochaeta africana DSM 8902 AFG37541.1YP_005475248.1 H9UJ48 Sprochaeta caldaria (strain ATCC AEJ20927.1YP_004699435.1 F8F2E5 51460/DSM 7334/H1) Sprochaeta caldaria (strainATCC AEJ18974.1 YP_004697482.1 F8F0B0 51460/DSM 7334/H1) Spirochaetacoccoides (strain ATCC AEC02997.1 YP_004412379.1 F4GLV6 BAA-1237/DSM17374/SPN1) Spirochaeta coccoides (strain ATCC AEC02807.1 YP_004412189.1F4GJR0 BAA-1237/DSM 17374/SPN1) Spirochaeta smaragdinae (strain DSMADK83104.1 YP_003805698.1 E1R9D5 11293/JCM 15392/SEBR 4228) Spirochaetasmaragdinae (strain DSM ADK82412.1 YP_003805006.1 E1RAP4 11293/JCM15392/SEBR 4228) Spirochaeta thermophila (strain ATCC ADN01075.1YP_003873348.1 E0RU19 49972/DSM 6192/RI 19.B1) Spirochaeta thermophilaDSM 6578 AEJ60373.1 YP_006044090.1 G0GBL4 Spirosoma linguale (strainATCC ADB42312.1 YP_003391111.1 D2QU30 33905/DSM 75/LMG 10896)Streptococcus anginosus 1_2_62CV EFW07929.1 ZP_08013620.1 E7GWK1Streptococcus anginosus CGUG 39159 EID21884.1 I0SET1 Streptococcusanginosus F0211 EFU22895.1 ZP_07863625.1 E6IZR2 Streptococcus anginosusSK52 = DSM EGL47971.1 ZP_08524336.1 F5TZ42 20563 Streptococcus australisATCC 700641 EFV99485.1 ZP_08021412.1 E7SBM6 EGU64265.1 Streptococcuscanis FSL Z3-227 EIQ82096.1 ZP_10274029.1 Streptococcus constellatussubsp. EID22796.1 I0SHE3 constellatus SK53 Streptococcus constellatussubsp. EGV09466.1 ZP_08762014.1 F9P6H6 pharyngis SK1060 = CCUG 46377Streptococcus criceti HS-6 EHI74170.1 ZP_09123331.1 G5JTU8 Streptococcuscristatus ATCC 51100 EFX53291.1 ZP_08059281.1 E8JTL6 EGU66254.1Streptococcus downei F0415 EFQ56787.1 ZP_07726381.1 E3CLH4 Streptococcusdysgalactiae subsp. ADX24753.1 YP_006013333.1 E8QAX7 equisimilis (strainATCC 12394/D166B) Streptococcus dysgalactiae subsp. BAH81730.1YP_002996944.1 C5WH65 equisimilis (strain GGS_124) Streptococcusdysgalactiae subsp. EGL49418.1 F5U565 equismilis SK1249 Streptococcusequi subsp. AEJ25504.1 F8IMR8 zooepidemicus (strain ATCC 35246/C74-63)Streptococcus equi subsp. ACG62550.1 YP_002123563.1 B4U3I3 zooepidemicus(strain MGCS10565) Streptococcus equines ATCC 9812 EFW88979.1ZP_08041402.1 E8JP85 Streptococcus gallolyticus subsp. EFM29278.1ZP_07464895.1 E0PL23 gallolyticus TX20005 Streptococcus ictaluri 707-05EHI69863.1 ZP_09126352.1 G5K2J5 Streptococcus infantarius (strain CJ18)AEZ62572.1 YP_005204043.1 H6PBS3 Streptococcus infantis ATCC 700779EFX36879.1 ZP_08061125.1 E8JZ60 EIG40319.1 Streptococcus infantis SK1076EGL85964.1 ZP_08523541.1 F5W0Y7 Streptococcus infantis SK1302 EFO55275.1ZP_07692775.1 E1M520 Streptococcus infantis SK970 EGV04542.1 F9PUI2Streptococcus infantis X EGV15183.1 F9PB80 Streptococcus intermediusSK54 BAM23377.1 YP_006469625.1 I0X1J6 EID82512.1 Streptococcus macacaeNCTC 11558 EHJ52132.1 ZP_09134350.1 G5JVK4 Streptococcus macedonicus(strain CCF02741.1 YP_005095067.1 H2A7K5 ACA-DC 198) Streptococcus mitis(strain B6) CBJ21968.1 YP_003445836.1 D3H7X6 Streptococcus mitis ATCC6249 EFM31215.1 ZP_07462962.1 E0PS01 Streptococcus mitis bv. 2 str.F0392 EGR93006.1 F9P0J2 Streptococcus mitis bv. 2 str. SK95 EGU67810.1F9LW41 Streptococcus mitis NCTC 12261 EFN95948.1 ZP_07638954.1 E1M0K5Streptococcus mitis SK1073 EGP65457.1 F9HDJ2 Streptococcus mitis SK1080EGP70417.1 F9HK06 Streptococcus mitis SK569 EGU71416.1 F9MHA3Streptococcus mitis SK575 EID27575.1 I0SW22 Streptococcus mitis SK579EID31778.1 I0T825 Streptococcus mitis SK597 EFO00396.1 ZP_07641986.1E1LSZ7 Streptococcus mitis SK616 EID24616.1 I0SML3 Streptococcus oralisSK10 EIC79352.1 I0QDK0 Streptococcus oralis SK100 EIC76735.1 I0Q633Streptococcus oralis SK1074 EID25784.1 I0SQY1 Streptococcus oralis SK255EGL90926.1 F5VTF6 Streptococcus oralis SK313 EGV00858.1 F9Q4H5Streptococcus oralis SK610 EIC75997.1 I0Q3Z5 Streptococcus parasanguinisF0449 EIG27302.1 Streptococcus parasanguinis (strain AEH55709.1YP_004621637.1 F8DI02 ATCC 15912/DSM 6778/CIP 104372 LMG 14537)Streptococcus parasanguinis ATCC EFX38996.1 ZP_08063273.1 E8K5A8 903Streptococcus parasanguinis F0405 EFQ55999.1 ZP_07726902.1 E3CB49Streptococcus parasanguinis SK236 EGU65274.1 F9M0Q9 Streptococcusparauberis (strain KCTC AEF25390.1 YP_004479062.1 F5ZIR6 11537)Streptococcus parauberis NCFD 2020 EGE54640.1 ZP_08246038.1 F1Z1C3Streptococcus peroris ATCC 700780 EFX40622.1 ZP_08065211.1 E8KB51Streptococcus pneumoniae (strain 670- ADM90954.1 YP_003879054.1 A5MHD16B) EDK68094.1 ZP_01830980.1 E0TMA5 EGI85205.1 F3VJ08 EHD49693.1 G6KXZ1EHD63537.1 G6M938 EHD88133.1 G6NUS3 EHE00949.1 G6QQ59 EHE60798.1 G6VMF7EHZ08811.1 H7K7G8 EIA01765.1 H7NWY1 EIA03628.1 H7P9A4 Streptococcuspneumoniae (strain ACO16116.1 YP_002740683.1 A5M825 70585) EDK66086.1ZP_01827724.1 C1C807 EHD28957.1 ZP_04524259.1 G6JBH8 EHD89063.1ZP_04598288.1 G6PTT6 EHE10731.1 G6RMA4 EHY96087.1 H7JGM5 EHZ58538.1H7MCK4 Streptococcus pneumoniae (strain ACA37604.1 YP_001694843.1 A5MT27Hungary 19A-6) EDK82213.1 ZP_01834726.1 B1ICK8 EHD56190.1 G6LGP3EHZ17150.1 H7I8B3 EHZ26304.1 H7KWU0 EHZ51454.1 H7LTH4 Streptococcuspneumoniae GA05245 EGI85461.1 F3WAV6 EHE02013.1 G6R2M6 EHZ03819.1 H7PKX9Streptococcus pneumoniae GA11663 EHE76579.1 G6P9A5 Streptococcuspneumoniae GA13637 EHD92416.1 G6Q076 Streptococcus pneumoniae GA40028EDT91262.1 ZP_02710611.1 B2DHG4 EHE29264.1 G6T4S1 EHZ39486.1 H7NP72EHZ97713.1 H7QAJ1 Streptococcus pneumoniae GA40563 EHZ44498.1 H7LG30Streptococcus pneumoniae GA41688 EHE25505.1 G6SS73 Streptococcuspneumoniae GA47373 EHE36709.1 G6TER8 Streptococcus pneumoniae GA47439EDT95056.1 ZP_02715455.1 B2DT86 EHE39175.1 G6TUT3 Streptococcuspneumoniae GA47461 EHZ60517.1 H7MHZ6 Streptococcus pneumoniae GA47522EHD39940.1 G6K6A5 EHZ64825.1 H7HCA4 EHZ94055.1 H7MPL4 Streptococcuspneumoniae GA47778 EHD60478.1 G6LTP3 EHE14708.1 G6RV07 EHE17320.1 G6RZ73EHE42733.1 G6U6L7 Streptococcus pneumoniae GA49194 EGJ14922.1 F3XKI1EHZ72974.1 H7J3Y0 EHZ90787.1 H7NER5 Streptococcus pneumoniae GA49542EDK79250.1 ZP_01822626.1 A5LTH7 EDT92444.1 ZP_02713772.1 B2DPR6EGI84194.1 F3VP30 EHD76303.1 G6NBR6 EHE37076.1 G6TMQ1 EHE51720.1 G6UNS9EHE67173.1 G6WCE5 EHZ48988.1 H7LJZ9 EHZ76888.1 H7NIU9 Streptococcusporcinus str. Jelinkova EGJ26555.1 ZP_08398558.1 F3LB38 176Streptococcus pseudopneumoniae AEL10828.1 YP_004768688.1 G0IAN6 (strainIS7493) Streptococcus pseudopneumoniae EID23674.1 ZP_09992237.1 I0SJX1SK674 EID70047.1 I0W0Y1 Streptococcus pseudoporcinus LQ 940- EFR44687.1ZP_07823857.1 E4L3R5 04 EHI65004.1 G5KAN5 Streptococcus pyogenes HKUEIK42042.1 QMH11M0907901 Streptococcus pyogenes Alab49 AEQ24391.1YP_006071945.1 G4R4C7 Streptococcus pyogenes ATCC 10782 EFM33381.1ZP_07460727.1 E0PWA2 Streptococcus pyogenes MGAS1882 AFC66139.1YP_005388837.1 H8HAK4 AFC68003.1 YP_005411534.1 H8HE06 Streptococcuspyogenes serotype M1 AAZ51384.1 YP_282129.1 Q48Z34 Streptococcuspyogenes serotype M12 ABF32069.1 YP_596613.1 Q1JC16 (strain MGAS9429)ABF35892.1 YP_600436.1 Q1JM00 Streptococcus pyogenes serotype M2ABF33948.1 YP_598492.1 Q1JH46 (strain MGAS10270) Streptococcus pyogenesserotype M28 AAX71858.1 YP_280213.1 Q48TU8 Streptococcus pyogenesserotype M4 ABF37868.1 YP_602412.1 Q1J6W5 (strain MGAS10750)Streptococcus pyogenes serotype M6 AAT86926.1 YP_060109.1 Q5XCD7Streptococcus salivarius (strain 57.1) AEJ53614.1 YP_006068477.1 F8HDR2EGX30167.1 G2GSH1 Streptococcus salivarius SK126 EEK10550.1ZP_04061476.1 C2LQT3 Streptococcus sanguinis ATCC 49296 EFU62475.1ZP_07888343.1 E6KNA8 Streptococcus sanguinis SK1056 EGJ39149.1 F3UB48Streptococcus sanguinis SK1057 EGF06788.1 F2BSB3 Streptococcus sanguinisSK1058 EGF21443.1 F2CLJ1 Streptococcus sanguinis SK1087 EGG40307.1F3SHX4 Streptococcus sanguinis SK115 EGD31794.1 F0I7V9 Streptococcussanguinis SK150 EGD36508.1 F0IMN8 Streptococcus sanguinis SK160EGD38300.1 F0IUP5 Streptococcus sanguinis SK330 EGF15598.1 F2C6E1Streptococcus sanguinis SK340 EGJ44393.1 F3UHS5 EGQ20720.1 F9E0L5EGQ24079.1 F9E949 Streptococcus sanguinis SK353 EFX93874.1 ZP_08087316.1E8KPS1 EGC23179.1 F0FDK9 Streptococcus sanguinis SK355 EGJ38546.1 F3US14Streptococcus sanguinis SK408 EGC24921.1 F0FJT3 EGF08624.1 F2BIW4EGF19580.1 F2CDE0 Streptococcus sanguinis SK49 EGJ38526.1 F3UY06Streptococcus sanguinis SK678 EGC27602.1 F0FR11 Streptococcus sanguinisSK72 EGD29398.1 F0I1T9 Streptococcus sp. SK140 EIF38589.1 ZP_10038759.1Streptococcus sp. SK643 EIF39120.1 ZP_10040082.1 Streptococcus sp. C300EFX56812.1 ZP_08050022.1 E9FHQ0 Streptococcus sp. M143 EFA24288.1ZP_06198674.1 D2EQA3 Streptococcus sp. M334 EFX59032.1 ZP_08050711.1E9FKM3 Streptococcus sp. oral taxon 056 str. EGP66993.1 ZP_08662553.1F9HGU8 F0418 Streptococcus sp. oral taxon 058 str. EHI77041.1ZP_09174472.1 G6C955 F0407 Streptococcus sp. oral taxon 071 str.EFM35756.1 ZP_07458299.1 E0Q0E1 73H25AP Streptococcus thermophilus(strain ABJ66404.1 YP_006340266.1 Q03K68 ATCC BAA-491/LMD-9) AFJ83601.1YP_820600.1 Streptococcus urinalis 2285-97 EHJ57402.1 ZP_09137413.1G5KGX7 Streptococcus vestibularis ATCC EFQ59772.1 ZP_07722949.1 E3CNS349124 EFX96303.1 ZP_08069523.1 E8KUL8 Tannerella forsythia (strain ATCCAEW20074.1 YP_005013402.1 G8UKW3 43037/JCM 10827/FDC 338) Bacteroidesforsythus Tepidanaerobacter acetatoxydans AEE92466.1 YP_004461773.1F4LT66 (strain DSM21804/JCM 16047/RE1) Thermincola potens (strain JR)ADG83236.1 YP_003641137.1 D5XAN2 Thermovirga lienii (strain ATCC BAA-AER67504.1 YP_004933601.1 G7V8P3 1197/DSM 17291/Cas60314) Treponema sp.JC4 EID85541.1 ZP_10009441.1 I0XA75 Turicibacter sanguinis PC909EFF63439.1 ZP_06622212.1 D4W6H2 Turicibacter sp. HGF1 EGC92139.1ZP_08167528.1 F0HEZ8 Victivallis vadensis ATCC BAA-548 EFA99410.1ZP_06244492.1 D1N9V2 Weeksella virosa (strain ATCC ADX67941.1YP_004238519.1 F0P329 43766/DSM 16922/JCM 21250/NBRC 16016/NCTC 11634/CL345/78) Weissella confusa LBAE C39-2 CCF29905.1 ZP_10257557.1 H1X5Q2Weissella paramesenteroides ATCC EER75253.1 ZP_04782492.1 C5R921 33313Weissella thailandensis fsh4-2 CCC57018.1 G0UGX7 Eukaryota Arabidopsislyrata subsp. lyrata (Lyre- EFH68720.1 XP_002892461.1 D7KIS7 leavedrock-cress) Arabidopsis lyrata subsp. lyrata (Lyre- EFH61940.1XP_002885681.1 D7L5U9 leaved rock-cress) Arabidopsis thaliana (mouse-earcress) CAA85388.1 Q42562 Arabidopsis thaliana (mouse-ear cress)CAA85387.1 Q42558 Arabidopsis thaliana (mouse-ear cress) AEE76980.1NP_189147.1 Q42561 BAB02069.1 BAD43868.1 CAA85389.1 Arachis hypogaea(peanut) ABO38556.1 A9P5P3 ABO38557.1 Arachis hypogaea (peanut)ABO38558.1 A9P5P5 Arachis hypogaea (peanut) ABO38554.1 A9P5P1 Arachishypogaea (peanut) ABO38555.1 A9P5P2 Brachypodium sylvaticum (falsebrome) ABL85052.1 A1YKG2 Brassica campestris (field mustard) AAC49002.1Q39402 Brassica juncea (Indian mustard) CAC14164.1 Q9FT16 (Sinapisjuncea) Camellia oleifera ACQ57189.1 C3W2Q2 Camellia oleifera ACQ57190.1C3W2Q3 Camellia oleifera ACQ63293.1 C3W2Q1 Camellia oleifera ACQ57188.1C3W2Q0 Camellia oleifera ACQ57187.1 C3W2P9 Capsicum annuum (bell pepper)ADH03021.1 D7RU32 Capsicum chinense (Scotch bonnet) AAG35064.1 Q9FPM5(bonnet pepper) Capsicum frutescens (cayenne papper) AEO12091.1 G3F052(Tabasco pepper) Chimonanthus praecox ADM18137.1 H9L9E6 Chlamydomonasreinhardtii EDP08596.1 XP_001696619.1 A8HY17 (Chlamydomonas smithii)Citrus sinensis (sweet orange) (Citrus AEX99667.1 H2ESB6 aurantium var.sinensis) Coccomyxa subellipsoidea C-169 EIE27817.1 I0ZAZ8 Cocosnucifera (coconut) AEM72519.1 G3ESU6 Cocos nucifera (coconut) AEM72520.1G3ESU7 Cocous nucifera (coconut) AEM72521.1 G3ESU8 Cuphea calophyllasubsp. mesostemon ABB71581.1 Q2A1N7 Cuphea calophylla subsp. mesostemonABB71579.1 Q2Q1N8 ABB71580.1 Cuphea hookeriana (cigar plant) AAC72882.1Q9ZTF8 Cuphea hookeriana (cigar plant) AAC72881.1 Q9ZTF9 Cupheahookeriana (cigar plant) AAC49269.1 Q39514 Cuphea hookeriana (cigarplant) AAC72883.1 Q9ZTF7 Cuphea lanceolata (cigar flower) CAA54060.1Q39534 Cuphea lanceolata (cigar flower) CAC19933.1 Q9FNS8 Cuphealanceolata (cigar flower) CAC19934.1 Q9FNS7 Cuphea lanceolata (cigarflower) CAB60830.1 Q9SMI9 Cuphea palustris AAC49180.1 Q39555 Cupheapalustris AAC49179.1 Q39554 Cuphea viscosissima AEM72523.1 G3ESV0 Cupheaviscosissima AEM72524.1 G3ESV1 Cuphea viscosissima AEM72522.1 G3ESU9Cuphea wrightii (Wright's waxweed) AAC49784.1 Q39663 Cuphea wrightii(Wright's waxweed) AAC49783.1 Q39662 Garcinia mangostana AAB51525.1O04794 Garcinia mangostana AAB51524.1 O04793 Garcinia mangostanaAAB51523.1 O04792 Glycine max (soybean) (Glycine ABD91726.1NP_001237802.1 B1MVG6 hispida) Glycine max (soybean) (Glycine ABI20759.1Q0GJK0 hispida) Glycine max (soybean) (Glycine ABI20760.1 Q0GJJ9hispida) Haematococcus pluvialis AEF13160.1 G9B653 Helianthus annuus(common CAC80371.1 Q8VXJ5 sunflower) Helianthus annuus (commonAAB88824.1 O48568 sunflower) AAX19377.1 AAX19378.1 AAX19379.1 AAX19380.1AAX19381.1 AAX19382.1 AAX19383.1 AAX19384.1 AAX19385.1 AAX19386.1AAX19387.1 Helianthus annuus (common AAQ08202.1 Q2UZT2 sunflower)Helianthus annuus (common CAC80370.1 Q8VXJ6 sunflower) Helianthus annuus(common AAQ08223.1 Q2UZT0 sunflower) AAQ08224.1 AAQ08225.1 AAQ08226.1Helianthus annuus (common AAL79361.1 Q6K1M5 sunflower) Helianthus annuus(common AAX54515.1 Q4KU00 sunflower) Helianthus annuus (commonAAX54514.1 Q4KU01 sunflower) Helianthus annuus (common AAX54516.1 Q4KTZ8sunflower) AAX54517.1 AAX54518.1 AAX54519.1 AAX54520.1 AAX54521.1AAX54522.1 AAX54523.1 AAX54524.1 AAX54525.1 AAX54526.1 AAX54527.1 Irisgermanica (flag) (fleur-de-lis) AAG43857.1 Q9FQY1 Iris germanica (flag)(fleur-de-lis) AAG43858.1 Q9FQY0 Iris germanica (flag) (fleur-de-lis)AAG43859.1 Q9FQX9 Iris tectorum AAG43860.1 Q9FQX8 Iris tectorumAAG43861.1 Q9FQX7 Iris tectorum AAL77443.1 Q8S9G4 Jatropha curcasABX82799.3 A9UFC5 Macadamia tetraphylla ADA79524.1 D2E6T0 Macadamiatetraphylla ACB29661.1 D5FFZ2 Medicago truncatula (barrel medic)AES91389.1 XP_003609192.1 G7JU47 (Medicago tribuloides) Myristicafragrans (nutmeg) AAB71729.1 O24419 Myristica fragrans (nutmeg)AAB71730.1 Q6I8R5 Nicotiana tabacum (common tobacco) AFE88232.1 H9CCH9Perilla frutescens (beefsteak mint) AAL77445.1 Q8SMI2 (Perillaocymoides) Populus tomentosa (Chinese white ABC47311.1 A1XAM4 poplar)Triticum aestivum (wheat) CAD32683.1 Q8L6B1 Ulmus americana (Americanelm) AAB71731.1 O24420 Umbellularia californica (California AAC49001.1Q41634 bay laurel) (Tetranthera californica) information obtained fromwww.enzyme.cbirc.iastate.edu (© Iowa State University of Science andTechnology; used with permission)

A method of altering the specificity of a plant acyl-ACP TE for at leastone of its substrates is also provided. For example, the specificity ofa plant acyl-ACP TE for at least one of its substrates can be increasedor decreased, even eliminated. The method comprises introducing into theplant acyl-ACP TE a substrate specificity-altering mutation in theregion corresponding to amino acids 118-167, such as from about aminoacid 118 to about amino acid 167, of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2 (see, SEQ ID NO:3in FIG. 1, starting at the amino acid position indicated by ▾).Alternatively, the region can correspond to amino acids 110-184, such asfrom about amino acid 110 to about amino acid 184, of the mature aminoacid of the Cuphea viscosissima acyl-ACP TE encoded by FatB2. Also,alternatively, the region can correspond to amino acids 110-205, such asfrom about amino acid 110 to about amino acid 205, of the mature aminoacid of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.“Corresponding to” is used herein to refer to an amino acid in anacyl-ACP TE, such as a plant acyl-ACP TE, which, when the amino acidsequence of the acyl-ACP TE is aligned with the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2, alignswith the position of the amino acid of the Cuphea viscosissima acyl-ACPTE to which reference is made by number. The amino acid in the acyl-ACPTE may or may not have the same numbered position as that in the matureamino acid sequence of the Cuphea viscosissima acyl-ACP TE encoded byFatB2. The method can comprise mutating at least one amino acidcorresponding to an amino acid selected from the group consisting ofamino acid 133, amino acid 142, and amino acid 143 of the mature aminoacid sequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.Mutating amino acid 133 to phenylalanine (F) or leucine (L) can increaseproduction of C8 fatty acids, mutating amino acid 133 to valine (V) oralanine (A) can increase production of C14/16 fatty acids, mutatingamino acid 142 to A and mutating amino acid 143 to serine (S) canincrease production of C8 fatty acids, and mutating both of amino acids142 and 143 to arginine (R) can increase production of C14/16 fattyacids. The method can further comprise mutating at least one amino acidcorresponding to an amino acid selected from the group consisting ofamino acid 110 and amino acid 184 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2. Mutating aminoacid 110 to F can increase production of C4/6 fatty acids, mutatingamino acid 110 to L can increase production of C8 fatty acids, mutatingamino acid 110 to V can increase production of C14/16 fatty acids, andmutating amino acid 184 to F can increase production of C8 fatty acids.The method can further comprise altering the level of activity of theplant acyl-ACP TE by a method comprising mutating at least one aminoacid corresponding to an amino acid selected from the group consistingof amino acid 173, amino acid 176, and amino acid 205 of the matureamino acid sequence of the Cuphea viscosissima acyl-ACP TE encoded byFatB2. Mutating amino acid 173 to F, mutating amino acid 176 to L,mutating amino acid 205 to F, or a combination of two or more of theforegoing can alter the level of activity of the plant acyl-ACP TE, suchas increase the level of activity of the plant acyl-ACP TE. Generallyspeaking, such mutations alter the level of activity of the plantacyl-ACP TE, such as increase the level of activity of the plantacyl-ACP TE, without altering the substrate specificity significantly,if at all. In other words, these mutations can alter the total amount offatty acids produced, such as increase the total amount of fatty acidsproduced, but do not significantly alter (if at all) the mol percentageof each fatty acid. Preferably, even desirably, the level of activity ofthe plant acyl-ACP TE is increased, rather than decreased.

In view of the foregoing, a method of altering the level of activity ofa plant acyl-ACP TE is also provided. For example, the activity level,e.g., thioesterase activity level, such as the total amount of fattyacids produced, of the plant acyl-ACP TE can be increased or decreasedcompared to the activity level of the corresponding wild-type TE. Analteration in the level of activity can be an increase in fatty acidproduction or a decrease in fatty acid production, irrespective ofwhether or not the mol percentage of each fatty acid changes or not.Preferably, even desirably, the level of activity of the plant acyl-ACPTE is increased, rather than decreased. The method comprises mutating atleast one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 173, amino acid 176, and amino acid 205of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2. Mutating amino acid 173 to F, mutating amino acid 176to L, mutating amino acid 205 to F, or a combination of two or more ofthe foregoing can alter the level of activity of the plant acyl-ACP TE,such as increase the level of activity of the plant acyl-ACP TE. Themethod can further comprise altering the specificity of the plantacyl-ACP TE by a method comprising introducing into the plant acyl-ACPTE a substrate specificity-altering mutation in the region correspondingto amino acids 118-167 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The method can comprisemutating at least one amino acid corresponding to an amino acid selectedfrom the group consisting of amino acid 133, amino acid 142, and aminoacid 143 of the mature amino acid sequence of the Cuphea viscosissimaacyl-ACP TE encoded by FatB2. Mutating amino acid 133 to F or L canincrease production of C8 fatty acids, mutating amino acid 133 to V or Acan increase production of C14/16 fatty acids, mutating amino acid 142to A and mutating amino acid 143 to S can increase production of C8fatty acids, and mutating both of amino acids 142 and 143 to R canincrease production of C14/16 fatty acids. The method can furthercomprise mutating at least one amino acid corresponding to an amino acidselected from the group consisting of amino acid 110 and amino acid 184of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2. Mutating amino acid 110 to F can increase productionof C4/6 fatty acids, mutating amino acid 110 to L can increaseproduction of C8 fatty acids, mutating amino acid 110 to V can increaseproduction of C14/16 fatty acids, and mutating amino acid 184 to F canincrease production of C8 fatty acids.

Also in view of the foregoing, an isolated or purified nucleic acidmolecule comprising a nucleotide sequence encoding a mutant acyl-ACP TEderived from a wild-type acyl-ACP TE, such as an acyl-ACP TE from FIG.5, FIG. 9, Table 1, Table 2, or www.enzyme.cbirc.iastate.edu (see, e.g.,family TE14; which website is incorporated herein by reference for itsteachings regarding acyl-ACP TEs), in particular an acyl-ACP TE from abacterium, e.g., an acyl-ACP TE from Bryantella formatexigens, is alsoprovided. The mutant acyl-ACP TE derived from wild-type Bryantellaformatexigens acyl-ACP TE comprises two or more amino acid mutationscomprising N169Y and S222I, and has increased thioesterase activitycompared to wild-type Bryantella formatexigens acyl-ACP TE.

Further in view of the foregoing, an isolated or purified nucleic acidmolecule comprising a nucleotide sequence encoding a chimeric Cupheaviscosissima acyl-ACP TE gene, which comprises a segment of anotheracyl-ACP TE gene, is provided. Any suitable acyl-ACP TE gene can serveas the source of the segment that is used to replace the segment of thewild-type Cuphea viscosissima acyl-ACP TE gene (see, e.g., FIG. 5, FIG.9, Table 1, Table 2, and www.enzyme.cbirc.iastate.edu (see, e.g., familyTE14), which website is hereby incorporated by reference for itsteachings regarding acyl-ACP TEs). Preferably, the acyl-ACP TE gene isanother Cuphea viscosissima acyl-ACP TE gene. The chimeric Cupheaviscosissima acyl-ACP TE gene preferably is a chimeric FatB1 gene or achimeric FatB2 gene. In this regard, preferably the chimeric CvFatB1gene comprises a segment of the CvFatB2 gene or the chimeric CvFatB2gene comprises a segment of the CvFatB2 gene.

Still further in view of the foregoing, an isolated or purified nucleicacid molecule comprising a nucleotide sequence encoding a mutant plantacyl-ACP TE, which comprises a substrate specificity-altering mutationin the region corresponding to amino acids 118-167, such as from aboutamino acid 118 to about amino acid 167, of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2, isprovided. Alternatively, the region can correspond to amino acids110-184, such as from about amino acid 110 to about amino acid 184, ofthe mature amino acid of the Cuphea viscosissima acyl-ACP TE encoded byFatB2. Also, alternatively, the region can correspond to amino acids110-205, such as from about amino acid 110 to about amino acid 205, ofthe mature amino acid of the Cuphea viscosissima acyl-ACP TE encoded byFatB2. Any suitable plant acyl-ACP TE gene can be mutated (see, e.g.,FIG. 5, FIG. 9, Table 1, Table 2, and www.enzyme.cbirc.iastate.edu (see,e.g., family TE14), which website is hereby incorporated by referencefor its teachings regarding acyl-ACP TEs). The isolated or purifiednucleic acid molecule can be a vector. The encoded mutant plant acyl-ACPTE can comprise a mutation of at least one amino acid corresponding toan amino acid selected from the group consisting of amino acid 133,amino acid 142, and amino acid 143 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2. The encoded mutantplant acyl-ACP TE can further comprise a mutation of at least one aminoacid corresponding to an amino acid selected from the group consistingof amino acid 110 and amino acid 184 of the mature amino acid sequenceof the Cuphea viscosissima acyl-ACP TE encoded by FatB2. The encodedmutant plant acyl-ACP TE can further comprise a level ofactivity-altering mutation of at least one amino acid corresponding toan amino acid selected from the group consisting of amino acid 173,amino acid 176, and amino acid 205 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2.

Still yet another isolated or purified nucleic acid molecule isprovided. The isolated or purified nucleic acid molecule comprises anucleotide sequence encoding a mutant plant acyl-ACP TE, which comprisesa level of activity-altering mutation (e.g., a mutation that alters thetotal amount of fatty acids produced, such as increases the total amountof fatty acids produced) of at least one amino acid corresponding to anamino acid selected from the group consisting of amino acid 173, aminoacid 176, and amino acid 205 of the mature amino acid sequence of theCuphea viscosissima acyl-ACP TE encoded by FatB2. Any suitable plantacyl-ACP TE gene can be mutated (see, e.g., FIG. 5, FIG. 9, Table 1,Table 2, and www.enzyme.cbirc.iastate.edu (see, e.g., family TE14, whichwebsite is hereby incorporated by reference for its teachings regardingacyl-ACP TEs). The isolated or purified nucleic acid molecule can be avector. The encoded mutant plant acyl-ACP TE can comprise a substratespecificity-altering mutation in the region corresponding to amino acids118-167, such as from about amino acid 118 to about amino acid 167, ofthe mature amino acid of the Cuphea viscosissima acyl-ACP TE encoded byFatB2. Alternatively, the region can correspond to amino acids 110-184,such as from about amino acid 110 to about amino acid 184, of the matureamino acid of the Cuphea viscosissima acyl-ACP TE encoded by FatB2. Alsoalternatively, the region can correspond to amino acids 110-205, such asfrom about amino acid 110 to about amino acid 205, of the mature aminoacid of the Cuphea viscosissima acyl-ACP TE encoded by FatB2. Theencoded mutant plant acyl-ACP TE can comprise a mutation of at least oneamino acid corresponding to an amino acid selected from the groupconsisting of amino acid 133, amino acid 142, and amino acid 143 of themature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2. The encoded mutant plant acyl-ACP TE can furthercomprise a substrate specificity-altering mutation of at least one aminoacid corresponding to an amino acid selected from the group consistingof amino acid 110 and amino acid 184 of the mature amino acid sequenceof the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

Mutations, such as substitutions, insertions, deletions, and/or sidechain modifications, can be introduced into the nucleotide and aminoacid sequences of the acyl-ACP TE using any suitable technique known inthe art, including site-directed mutagenesis (Wu, ed., Meth. Enzymol.217, Academic Press (1993)). Alternatively, domains can be swappedbetween acyl-ACP TE genes (for example, when creating chimeras).Non-naturally occurring nucleotides and amino acids also can be used.Mutations to the nucleotide sequence should not place the sequence outof reading frame and should not create complementary regions that couldproduce secondary mRNA structures. The mutant or chimeric acyl-ACP TEmay have altered substrate specificity, e.g., reacts with an acyl-ACPsubstrate that differs in chain length, degree of saturation, orpresence/absence of a side group (e.g., methyl group), from that whichis acted upon by the wild-type (also referred to as “native”) acyl-ACPTE. Alternatively, the mutant or chimeric acyl-ACP TE may have alteredrelative substrate specificity between two or more substrates, both ofwhich are acted upon by the wild-type acyl-ACP TE. Both types ofalterations in substrate specificity are encompassed by references toalterations of substrate specificity and substratespecificity-alterating mutations herein. Alternatively or additionallyto altered substrate specificity, the mutant or chimeric acyl-ACP TE mayhave an altered activity level, e.g., level of thioesterase activity,such as the total amount of fatty acids produced, including increased ordecreased activity. Altered substrate specificity and altered activitycan be detected by expression of the mutant thioesterase in E. coli, forexample, and assay of enzyme activity.

A nucleotide sequence encoding all or a part of an acyl-ACP TE can bechemically synthesized, such as by the phosphoramidite method (Beaucageet al., Tetrahedron Letters 22: 1859-1869 (1981); and Matthes et al.,EMBO J. 3: 801-805 (1984)). Polynucleotides can be synthesized,purified, annealed to their complementary strand, ligated, and then,optionally, cloned into suitable vectors.

The isolated or purified nucleic acid molecule comprising a nucleotidesequence encoding a mutant/chimeric acyl-ACP TE can be a vector. Thevector can contain, and preferably does contain, transcription andtranslation control regions. A promoter can be constitutive orregulatable, such as inducible. Additional sequences that can be presentin the vector include pre-processing sequences, such as transit peptidesequences and plastid transit peptide sequences.

The acyl-ACP TEs and mutant/chimeric acyl-ACP TEs identified herein canbe used in whole or in part as probes in hybridization assays toidentify other TEs that can be used in the methods described herein. TheTEs or fragments thereof also can be used as primers to amplify targetDNA, such as by polymerase chain reaction (PCR) and other nucleic acidamplification methods. See, e.g., Sambrook et al., Molecular Cloning: ALaboratory Manual, 3^(rd) ed., Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y. (2001); Ausubel et al., eds., Short Protocols inMolecular Biology, 5^(th) ed., John Wiley & Sons (2002).

The nucleic acid molecule comprising a nucleotide sequence encoding anacyl-ACP TE or a mutant/chimeric acyl-ACP TE can be introduced into ahost cell or a host organism using any suitable technique as is known inthe art. See, e.g., Sambrook et al., Molecular Cloning: A LaboratoryManual, 3^(rd) ed., Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y. (2001); Ausubel et al., eds., Short Protocols in MolecularBiology, 5^(th) ed., John Wiley & Sons (2002). Such methods includemicroinjection, DNA particle bombardment, electroporation, liposomefusion, Agrobacterium-mediated transformation, and methods exemplifiedherein. Depending on the host cell or the host organism, one method canbe preferred over another as readily appreciated by one of ordinaryskill in the art. The nucleotide sequence can be codon-optimized for therecipient host cell or organism.

In view of the above, a host cell comprising an above-described isolatedor purified nucleic acid molecule is also provided. The host cell ororganism can be any suitable host cell or organism. The host cell ororganism can be prokaryotic or eukaryotic, unicellular or multicellular,and undifferentiated or differentiated. If large-scale production ofshort-chain fatty acids is desired, e.g., as a source of biofuel,bacteria (see, e.g., U.S. Pat. App. Pub. No. 2012/0164700, whichdiscloses examples of cyanobacteria, and U.S. Pat. App. Pub. No.2009/0298143, which discloses methods of expression in bacteria, andboth of which are hereby incorporated by reference for their teachingsregarding same), yeast (see, e.g., U.S. Pat. App. Pub. No. 2011/0294174,which discloses examples of yeast in Table 26 and other fungi in Table27 and which is hereby incorporated by reference for its teachingsregarding same), and algae (see, e.g., U.S. Pat. App. Pub. No.2011/0294174, which discloses examples of algae in Table 1 and which ishereby incorporated by reference for its teachings regarding same; also,see U.S. Pat. No. 7,935,515 and U.S. Pat. App. Pub. No. 2012/0164700,which disclose methods of expressing TEs in microalgae and examples ofmicroalgae and which are hereby incorporated by reference for theirteachings regarding same; see, also, U.S. Pat. App. Pub. No.2009/0317878, which is hereby incorporated by reference for itsteachings regarding expression of genes in algae) can be preferred. Apreferred bacterium is Escherichia coli, in particular the strain K27. Apreferred yeast is Saccharomyces cerevisiae. Alternatively, a crop plant(e.g., maize), such as an oilseed crop plant or a seed cell thereof, canbe preferred (see, e.g., U.S. Pat. No. 7,504,563, which disclosesexpression of a nucleic acid encoding a thioesterase in soybean seed andwhich is incorporated herein for its teachings regarding same). See,also, U.S. Pat. App. Pub. No. 2010/0154293, which discloses otherexamples of host cells in paragraph [0080] and which is incorporatedherein by reference for its teachings regarding same.

Fatty acids can be harvested, or otherwise collected (e.g., isolationfrom media containing bacteria that secrete the fatty acids), from hostcells or organisms by any convenient method. Cells can belysed/disrupted (e.g., heat, enzymes, ultrasound, mechanical lysis,osmotic shock, acid/base addition, or infection with a lytic virus), andfatty acids can be separated from cell mass by centrifugation andextraction (e.g., extraction with hydrophobic solvent, liquefaction,supercritical CO₂ extraction, or hexane extraction after freeze-dryingand pulverization) and further processed/refined as necessary. See,e.g., U.S. Pat. No. 7,935,515 and U.S. Pat. App. Pub. No. 2012/0135479,which are incorporated specifically by reference for their teachingsregarding same.

An isolated or purified mutant acyl-ACP TE derived from a wild-typeacyl-ACP TE, such as an acyl-ACP TE from FIG. 5, FIG. 9, Table 1, Table2, or www.enzyme.cbirc.iastate.edu (see, e.g., family TE14; whichwebsite is incorporated by reference herein for its teachings regardingacyl-ACP TEs), in particular an acyl-ACP TE from a bacterium, e.g., anacyl-ACP TE from Bryantella formatexigens, is also provided. The mutantacyl-ACP TE derived from wild-type Bryantella formatexigens acyl-ACP TEcomprises two or more amino acid mutations comprising N169Y and S222I,and has increased thioesterase activity compared to wild-type Bryantellaformatexigens acyl-ACP TE. Preferably, the mutant acyl-ACP TE derivedfrom wild-type Bryantella formatexigens acyl-ACP TE has alteredsubstrate specificity such that it increases production of short-chainfatty acids. Depending on the particular acyl-ACP TE (e.g., an acyl-ACPTE from FIG. 5, FIG. 9, Table 1, Table 2, orwww.enzyme.cbirc.iastate.edu (see, e.g., family TE14; which website isincorporated by reference herein for its teachings regarding acyl-ACPTEs), such as acyl-ACP TE from a bacterium) that has been mutated, suchmutants can have altered substrate specificity, such as alteredsubstrate specificity that results in increased production ofshort-chain fatty acids or fatty acids of longer chain length, and/oraltered level of activity, e.g., thioesterase activity, such as thetotal amount of fatty acids produced. Mutants can be derived fromwild-type acyl-ACP TEs in accordance with methods known in the art(e.g., site-directed mutagenesis) and exemplified herein. Due to thedegeneracy of the genetic code, the same amino acid sequence can beencoded by nucleotide sequences that vary quite a bit.

An isolated or purified chimeric Cuphea viscosissima acyl-ACP TE, whichcomprises a segment of another acyl-ACP TE, is also provided. Anysuitable acyl-ACP TE can serve as the source of the segment that is usedto replace the segment of the wild-type Cuphea viscosissima acyl-ACP TE(see, e.g., an acyl-ACP TE from FIG. 5, FIG. 9, Table 1, Table 2, orwww.enzyme.cbirc.iastate.edu (see, e.g., family TE14; which website isincorporated by reference herein for its teachings regarding acyl-ACPTEs). Preferably, the acyl-ACP TE is another Cuphea viscosissimaacyl-ACP TE. In this regard, the chimera can be made in accordance withmethods known in the art, such as at the level of DNA or protein,including synthesis. Preferably, the chimera is a chimera of the TEencoded by a FatB1 gene or a chimera of the TE encoded by a FatB2 gene.In this regard, the chimera can be a chimera of the TE encoded by theCvFatB1 gene comprising a segment of the TE encoded by the CvFatB2 geneor a chimera of the TE encoded by the CvFatB2 gene comprising a segmentof the TE encoded by the CvFatB1 gene.

An isolated or purified mutant plant acyl-ACP TE, which comprises asubstrate specificity-altering mutation in the region corresponding toamino acids 118-167, such as from about amino acid 110 to about aminoacid 167, of the mature amino acid sequence of the Cuphea viscosissimaacyl-ACP TE encoded by FatB2, is also provided. Alternatively, theregion can correspond to amino acids 110-184, such as from about aminoacid 110 to about amino acid 184, of the mature amino acid of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. Also, alternatively, theregion can correspond to amino acids 110-205, such as from about aminoacid 110 to about amino acid 205, of the mature amino acid of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The mutant TE can comprise amutation of at least one amino acid corresponding to an amino acidselected from the group consisting of amino acid 133, amino acid 142,and amino acid 143 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The mutant TE can furthercomprise a mutation of at least one amino acid corresponding to an aminoacid selected from the group consisting of amino acid 110 and amino acid184 of the mature amino acid sequence of the Cuphea viscosissimaacyl-ACP TE encoded by FatB2. The mutant TE can further comprise a levelof activity-altering mutation of at least one amino acid correspondingto an amino acid selected from the group consisting of amino acid 173,amino acid 176, and amino acid 205 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2.

Yet another isolated or purified mutant plant acyl-ACP TE is provided.The isolated or purified mutant plant acyl-ACP TE comprises a level ofactivity-altering mutation of at least one amino acid corresponding toan amino acid selected from the group consisting of amino acid 173,amino acid 176, and amino acid 205 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2. The mutant TE canfurther comprise a substrate specificity-altering mutation in the regioncorresponding to amino acids 118-167, such as from about amino acid 118to about amino acid 167, of the mature amino acid of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. Alternatively, the region cancorrespond to amino acids 110-184, such as from about amino acid 110 toabout amino acid 184, of the mature amino acid of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. Also, alternatively, theregion can correspond to amino acids 110-205, such as from about aminoacid 110 to about amino acid 205, of the mature amino acid of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The mutant TE can comprise amutation of at least one amino acid corresponding to an amino acidselected from the group consisting of amino acid 133, amino acid 142,and amino acid 143 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2. The mutant TE can furthercomprise a substrate specificity-altering mutation of at least one aminoacid corresponding to an amino acid selected from the group consistingof amino acid 110 and amino acid 184 of the mature amino acid sequenceof the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

Once sequenced, polypeptides can be synthesized using methods known inthe art, such as, for example, exclusive solid phase synthesis, partialsolid phase synthesis, fragment condensation, and classical solutionsynthesis. See, e.g., Merrifield, J. Am. Chem. Soc. 85: 2149 (1963), andStewart and Young in Solid Phase Peptide Syntheses (2nd Ed., PierceChemical Company, 1984). Automated peptide synthesizers are commerciallyavailable, as are services that make peptides to order.

EXAMPLES

The following examples serve to illustrate the present disclosure. Theexamples are not intended to limit the scope of the claimed invention inany way.

Example 1

This example describes the functional characterization of diverseacyl-ACP TEs rationally chosen based on phylogenetic classification ofthe TEs.

Sequences from Family TE14 (Cantu et al. (2010), supra) in the ThYmedatabase (www.enzyme.cbirc.iastate.edu) were downloaded from the GenBank(Benson et al., Nucleic Acids Res. 39 (suppl. 1): D32-D37 (2011)) andUniProt (UniProt Consortium: The universal protein resource (UniProt) in2010, Nucleic Acids Res. 38: D142-D148 (2010)) databases. Fragments andincomplete sequences were removed, yielding 360 acyl-ACP TE sequences. Amultiple sequence alignment (MSA) was generated from catalytic domainsof these sequences using MUSCLE 3.6 (Edgar, Nucleic Acids Res. 32:1792-1797 (2004)) with default parameters. An unrooted phylogenetic treebased on the MSA was built using Molecular Evolutionary GeneticsAnalysis 4 (MEGA4) (Tamura et al., Mol. Biol. Evol. 24: 1596-1599(2007)).

The minimum evolution algorithm was used due to its high effectivenesswith large data sets (Desper et al., J. Comput. Biol. 9: 687-705(2002)), gaps were subjected to pairwise deletion, and an amino acidJones-Taylor-Thornton (JTT) (Jones et al., Comput. Appl. Biosci. 8:275-282 (1992)) distance model was chosen. The phylogenetic tree wasfurther verified by a bootstrap test with 1,000 replicates. Thebootstrapped consensus tree was qualitatively analyzed and broken intoapparent subfamilies. Statistical analysis was conducted to show thatall sequences within a subfamily were more closely related to each otherthan to sequences in other subfamilies. Based on the MSA, JTT distancesbetween all sequences were calculated and arranged into a j×j matrix,where j is the total number of sequences. Inter-subfamily distances andvariances were determined using this matrix. For each apparentsubfamily, a smaller k×k matrix, where k is the number of sequences in agiven subfamily, was calculated. From this, intra-subfamily meandistances and variances were determined. These values were applied tothe following equation to determine z:

$z = \frac{{\overset{\_}{x}}_{ij} - {( {{\overset{\_}{x}}_{ii} + {\overset{\_}{x}}_{jj}} )/2}}{\sqrt{\frac{\sigma_{i}^{2}}{n_{ij}} + \frac{\sigma_{ii}^{2}}{n_{i}} + \frac{\sigma_{jj}^{2}}{n_{j}}}}$

where x _(ij), x _(ii), and x _(jj) are the inter- and intra-subfamilymean JTT distances, n_(ij), n_(ii), and n_(jj) are the total number oftaxa used for each x value, and σ_(i) ², σ_(ii) ², and σ_(jj) ² are thepooled inter- and intra-subfamily variances (Mertz et al., Biopolymers79: 197-206 (2005)).

A z-value >3.3 between two subfamilies shows that the difference betweenthem is statistically significant to p<0.001. If a z-value between twoapparent subfamilies were <3.3, alternative apparent subfamilies werechosen and/or individual sequences were removed, and the statisticalcalculations were repeated. Subfamilies were finally defined with aphylogenetic tree in which all z-values exceeded 3.3, sometimes leavingsome sequences outside any subfamily (i.e. non-grouped sequences) (seeTable 2).

TABLE 2 Total activity of synthesized and cloned acyl-ACP TEs TotalFatty ACC No. Acids Subfamily or Name Organism Rationale forsynthesis^(a) (nmol/mL)^(b) Kingdom: Planta A AAC49179^(c,d) Cupheapalustris A (Bimodal specificity for C8 and C10 708 ± 45 substrates)Dehesh et al., Plant Physiol. 110: 203-210 (1996) AAB71731 Ulmus A(Broad specificity; highest activity on 1098 ± 62  Americana C10 andC16) Voelker et al., Plant Physiol. 114: 669-677 (1997) AAG43857 Irisgermanica B 261 ± 20 AAG43858 Iris germanica B 14.8 ± 4.6 EER87824Sorghum bicolor B (Member of a Subfamily A Poeceae 126 ± 13 TE cluster)EER88593 Sorghum bicolor B (Member of a Subfamily A Poeceae 90.7 ± 8.0TE cluster) CnFatB1 Cocos nucifera C 130 ± 12 CnFatB2 Cocos nucifera C572 ± 32 CnFatB3 Cocos nucifera C 200 ± 11 CvFatB1 Cuphea C 79.2 ± 9.7viscosissima CvFatB2 Cuphea C 249 ± 9  viscosissima CvFatB3 Cuphea C18.9 ± 2.1 viscosissima AAD42220 Elaeis C 36.7 ± 3.8 guineensis BEDQ65090 Physcomitrella B (Member of novel plant subfamily) 380 ± 29patens EER96252 Sorghum bicolor B (Member of novel plant subfamily) 175± 11 EES11622 Sorghum bicolor B (Member of novel plant subfamily)  9.43± 2.03 D EEH52851 Micromonas B 16.3 ± 1.6 pusilla Kingdom: Bacteria EACL08376 Desulfovibrio D (Medium-chain linear, branched, and 330 ± 9 vulgaris hydroxy fatty acids) Ratledge et al., Microbial Lipids, Vol. 1,Academic Press, San Diego, CA (1988) F CAH09236 Bacteroides D (Hydroxyfatty acids) 215 ± 6  fragilis Ratledge et al., Microbial Lipids, Vol.1, Academic Press, San Diego, CA (1988) ABR43801 Parabacteroides D(Branched and branched hydroxy 70.3 ± 4.4 distasonis fatty acids)Sakamoto et al., Int. J. Syst. Evol. Microbiol. 57: 293-296 (2007)AAO77182^(e) Bacteroides D (Anteiso-branched and hydroxy fatty 60.4 ±2.9 thetaiotaomicron acids) Ratledge et al., Microbial Lipids, Vol. 1,Academic Press, San Diego, CA (1988) G ABG82470 Clostridium D(Medium-chain fatty acids) 72.0 ± 9.5 perfringens Moss et al., Appl.Microbiol. 15: 390-397 (1967) H EEG55387 Clostridium B 25.9 ± 4.2asparagiforme EET61113 Bryantella B 381 ± 3  formatexigens I EDV77528Geobacillus sp. D (Iso-branched fatty acids)  64.9 ± 12.0 Rahman et al.,BMC Microbiol. 2007: 7 (2007) J BAH81730 Streptococcus D (Medium-chainand cyclic propane 623 ± 14 dysgalactiae ring fatty acids) Ratledge etal., Microbial Lipids, Vol. 1, Academic Press, San Diego, CA (1988)ABJ63754 Lactobacillus D (Medium-chain and cyclic propane 710 ± 10brevis ring fatty acids) Johnsson et al., Appl. Environ. Microb. 61:4497-4499 (1995) CAD63310^(e) Lactobacillus D (Medium-chain 3′-hydroxyfatty 436 ± 10 plantarum acids) Johnsson et al., Appl. Environ. Microb.61: 4497-4499 (1995); Sjogren et al., Appl. Environ. Microb. 69:7554-7557 (2003) Non- EEI82564 Anaerococcus D (Organism produces butyricacid) 1381 ± 146 grouped tetradius Murdoch et al., J. Med. Microbiol.34: 295-308 (1991) CAE80300 Bdellovibrio D (Straight-chain odd-numberedfatty 333 ± 18 bacteriovorus acids) Ratledge et al., Microbial Lipids,Vol. 1, Academic Press, San Diego, CA (1988) ABN54268 Clostridium D(Branched-chain fatty acids) 97.7 ± 3.2 thermocellum Ratledge et al.,Microbial Lipids, Vol. 1, Academic Press, San Diego, CA (1988) ^(a)A:Functionally characterized TEs; B: TE does not group near characterizedTEs and/or no organism lipid profile information is available; C: TEscloned from organisms known to produce MCFAs; D: Organism's lipidprofile used and predominant fatty acid constituents identified in theorganism are listed in parentheses. ^(b)The data are represented as mean± standard error (n = 4). ^(c)All but the three C. nucifera sequenceswere codon-optimized for expression in E. coli. ^(d)Transit peptideswere removed from all plant sequences. ^(e)Acyl-ACP TEs with knowncrystal structures. TEs were expressed in E. coli K27, and free fattyacids (FAs) that accumulated in the medium were analyzed by GC-MS.

All sequences within individual subfamilies were aligned using MUSCLE3.6, and rooted phylogenetic trees were built in MEGA4 with the sametree and bootstrap parameters as described above. A few sequences fromanother subfamily (that with the highest z-value) were chosen to rootindividual subfamily trees.

A total of 360 amino acid sequences belonging to Family TE14 (Cantu etal. (2010), supra) were subjected to phylogenetic analysis and groupedinto subfamilies. A subfamily is defined as having at least fivesequences from different species, and it must pass the statistical testsdescribed in the experimental procedures. Ten subfamilies met thesecriteria, accounting for 326 TE sequences; in addition 34 TE sequencescould not be grouped into any of these subfamilies. All z-valueswere >3.4, ranging from 3.41 to 29.7, and mean distances betweendifferent subfamilies were larger than those within subfamilies.

Family TE14 contains acyl-ACP TEs that had previously been characterizedfrom plants and classified into two types, FatA and FatB (Jones et al.(1995), supra). Of the ten subfamilies identified, Subfamilies A, B, andC are comprised of acyl-ACP TEs found in plants. All experimentallycharacterized sequences previously classified as FatB acyl-ACP TEs makeup ˜25% of Subfamily A, which contains 81 angiosperm-sourced sequences.The coconut and C. viscosissima acyl-ACP TEs identified also belong tothis subfamily. Subfamily B, which comprises 21 sequences primarilysourced from angiosperms as well as from the moss Physcomitrella patens,represents a potentially novel plant acyl-ACP TE subfamily with noprevious experimental or phylogenetic characterization. Plant FatAacyl-ACP TEs, which act on long-chain acyl-ACP molecules, especiallyoleoyl-ACP (Jones et al. (1995), supra), belong to the 32-memberSubfamily C. As with Subfamily B, the six green algal sequences fromChlamydomonas, Ostreococcus, and Micromonas that comprise Subfamily Dhave not been experimentally characterized.

Unlike several plant acyl-ACP TEs, no bacterial acyl-ACP TEs had beenpreviously functionally characterized. A total of 186 bacterial acyl-ACPTE sequences were classified into six subfamilies (Subfamily E-SubfamilyJ). All 17 acyl-ACP TE sequences from gram-negative bacteria are inSubfamily E, which includes sequences from halophilic (Salinibacter andRhodothermus), sulfate-reducing (Desulfovibrio, Desulfohalobium, andDesulfonatronospira), chemo-organotrophic (Spirosoma), metal-reducing(Anaeromyxobacter, Geobacter, and Pelobacter), and marine (Microscilla)bacteria. Subfamily F consists of 24 sequences, mainly from Bacteroidesbut also from other related bacteria. Protein Data Bank (PDB) structure2ESS, obtained from a structural genomic effort, is part of thissubfamily. Subfamily G and Subfamily H have 31 and 27 sequences,respectively, primarily from Clostridium. Subfamily I is comprised ofeight sequences from six genera. Gram-positive lactic acid bacteria,almost completely from the genera Lactobacillus, Enterococcus, andStreptococcus, are part of Subfamily J (79 sequences). PDB:20WN, thesecond bacterial acyl-ACP TE structure obtained from a structuralgenomic effort, appears in this family. Although the two known FamilyTE14 crystal structures (PDB:2ESS in Subfamily F and PDB:2OWN inSubfamily J) are from organisms in widely separated subfamilies, theyare highly similar, as may be expected since they are members of thesame enzyme family.

Some Family TE14 sequences are not grouped into any subfamily becausetheir inclusion decreased z-values below acceptable limits. Theseinclude two plant and four moss sequences adjacent to Subfamilies A andC, and 28 bacterial sequences more closely related to Subfamilies E toI. No experimental work had previously been done on any of thesesequences.

Upon generating the phylogenetic relationships among the 360 acyl-ACP TEsequences predicted or experimentally placed in Family TE14, 25 werechosen for experimental characterization. Of these, the cDNA for 24 wassynthesized, while the cDNA of the Elaeis guineensis (oil palm) acyl-ACPTE was isolated from a phage cDNA library previously constructed frommRNA isolated from the developing fruit of Indonesian-sourced oil palm.

The selection of acyl-ACP TEs to characterize was based upon the primarystructure-based phylogenetic relationships among the enzymes, along withknowledge of the fatty acid profile of the source organisms of theseacyl-ACP TEs. Briefly, at least one TE was characterized from each ofthe ten subfamilies except for Subfamily C, whose members appear to bespecific for oleoyl-ACP substrates. For subfamilies that containacyl-ACP TEs originating from organisms without any known fatty aciddata, or from organisms where acyl-ACP TEs were not previouslycharacterized, acyl-ACP TE sequences that are evolutionarily distantfrom each other within each subfamily were selected for furtherinvestigation. For example, within Subfamily A there are two distinctand separate groupings of acyl-ACP TEs that are derived from the Poaceaefamily, for which there is no functional characterization (see Table 2).One grouping contains one sorghum acyl-ACP TE sequence(GenBank:EER87824) and the other contains two (GenBank:EER88593 andGenBank:EES04698). To explore this structural divergence as an indicatorof potential functional divergence in substrate specificities, one eachof these Subfamily A sorghum acyl-ACP TEs (GenBank:EER87824 andGenBank:EER88593) and the two Subfamily B sorghum acyl-ACP TEs wereexpressed and functionally characterized.

Example 2

This example describes the cloning of acyl-ACP TEs from Cocus nucifera(coconut) and Cuphea viscosissima.

Coconut fruits of different developmental stages were obtained from theUSDA-ARS-SHRS National Germplasm Repository (Miami, Fla., USA). Seeds ofC. viscosissima were obtained from the North Central Regional PlantIntroduction Station (NCRPIS, Ames, Iowa, USA). They were treatedovernight with 0.1 mM gibberellic acid and then germinated in a growthchamber (Environmental Growth Chambers, Chagrin Falls, Ohio) with 12hours of illumination at 25° C. followed by 12 hours of darkness at 15°C. Seedlings were transplanted into soil and cultivated at NCRPIS. Seedsat different developmental stages were collected and flash-frozen inliquid nitrogen.

Acyl-ACP TE cDNAs were cloned from C. viscosissima and coconut via ahomologous cloning strategy. MSAs of plant TE14 sequences revealed twoconserved regions (RYPTWGD [SEQ ID NO: 7] and NQHVNNVK [SEQ ID NO: 8]),from which two degenerate primers, DP-F3 (5′-AGNTAYCCNACNTGGGGNGA-3′[SEQ ID NO: 9]) and DP-R3 (5′-TACTTNACRTTRTTNACRTGYTGRTT-3′ [SEQ ID NO:10]), were designed. RNA was extracted from endosperm of nearly maturecoconuts and immature seeds of C. viscosissima using the total RNA(plant) kit (IBI Scientific, Peosta, Iowa, USA). RNA wasreverse-transcribed to cDNA using the SuperScript™ first-strandsynthesis system for RT-PCR kit (Invitrogen, Carlsberg, Calif., USA).PCR was performed in a 50-μL reaction mixture containing 20 ng cDNA,1×Pfx buffer, 1 mM MgSO₄, 0.3 mM dNTP, 5.12 μM DP-F3 and DP-R3 primers,and 0.5 U Pfx polymerase (Invitrogen) using a cycling program of 94° C.for four minutes, 35 cycles of 94° C. for 30 seconds, 52° C. for 30seconds and 72° C. for 45 seconds, and a final extension step of 72° C.for five minutes. The expected ˜350-bp products were identified byagarose gel electrophoresis, and their DNA bands were recovered usingthe QiaQuick gel extraction kit (Qiagen, Valencia, Calif., USA) andcloned into the pENTR TOPO TA vector (Invitrogen). Using primersdesigned from the sequences of the cloned 350-bp fragments, the 5′- and3′-ends of the cDNAs were obtained using the SMARTer RACE (rapidamplification of the cDNA ends) cDNA amplification kit (Takara Bio,Otsu, Japan).

For each acyl-ACP TE sequence, the full-length cDNA, minus theN-terminal chloroplast transit peptide, was amplified by PCR withprimers engineered to introduce Bam HI and Eco RI restriction sites atthe 5′- and 3′-ends, respectively. The PCR-amplified products weredigested with Bam HI and Eco RI and cloned into the correspondingrestriction sites of the pUC57 vector, which placed the acyl-ACP TEsequence under the transcriptional control of the lacZ promoter. Thesequence of each construct was confirmed by sequencing both strands.Confirmed expression vectors of coconut genes were transformed into E.coli strain K27, while sequences of C. viscosissima acyl-ACP TEs weresynthesized after being codon-optimized for expression in E. coli usingthe OptimumGene codon optimization program provided by GenScript USA(Piscataway, N.J., USA).

MCFAs are abundant in the oil produced in fruits of coconut (i.e.,predominantly C12 and C14 and a small amount (0.2-1%) of C6 fatty acids(Kumar et al., J. Food Qual. 32: 158-176 (2009); Kumar et al., IndianCoconut J. 37: 4-14 (2006); and Kumar et al., Trop. Agr. 81: 34-40(2004)) and seeds of C. viscosissima (i.e., predominantly C8 and C10fatty acids (Phippen et al., Ind. Crop Prod. 24: 52-59 (2006)).Therefore, acyl-ACP TEs in the seeds of these species are predicted tobe specific for medium-chain acyl-ACPs. Acyl-ACP TE sequences wereisolated from coconut and C. viscosissima by a homologous cloningstrategy. Using degenerate primers, which were designed from conservedregions of plant TE14 family enzymes, a 350-bp fragment in the middle ofthe mRNAs was amplified from cDNA generated from both developing coconutendosperm and C. viscosissima seeds. Sequencing of cloned PCR productsidentified three new acyl-ACP TE sequences each from coconut and C.viscosissima. The full-length cDNA sequences were obtained by RACE forthree acyl-ACP TEs [CnFatB1 (JF338903), CnFatB2 (JF338904), and CnFatB3(JF338905)] from coconut and three [CvFatB1 (JF338906), CvFatB2(JF338907), and CvFatB3 (JF338908)] from C. viscosissima.

The predicted open reading frames of coconut and C. viscosissimaacyl-ACP TE cDNAs were identified. They encode pre-proteins of 412 to423 amino acids, with calculated molecular weights of 45.8 to 46.5 kDaand theoretical pIs of 6.4 to 8.8. Plant acyl-ACP TEs arenuclear-encoded, plastid-targeted proteins with an N-terminalplastid-targeting peptide extension (Voelker et al. (1992), supra). Foreach of the cloned coconut and C. viscosissima acyl-ACP TEs, theputative plastid-targeting peptide cleavage site was located on theN-terminal side of the conserved sequence LPDW, as proposed for manyother plant acyl-ACP TEs (Jones et al. (1995), supra; Sanchez-Garcia(2010), supra; Dormann et al. (1995), supra; Jha et al., Plant Physiol.Biochem. 44: 645-655 (2006); and Moreno-Perez et al., Plant Physiol.Biochem. 49: 82-87 (2011)). These yield predicted mature proteins of 323to 331 amino acid residues (Huynh et al., Plant Physiol. Biochem. 40:1-9(2002)), with calculated molecular weights of 36.6 to 37.5 kDa andtheoretical pIs of 5.4 to 7.3. Alignment of the deduced amino acidsequences of coconut and C. viscosissima acyl-ACP TE cDNAs showed that,except for the plastid-targeting peptide sequences and very near theC-terminus, the sequences are co-linear and share very high identity(63-86%) within a species. These sequences cluster within Subfamily A.

Example 3

This example describes in vivo activity assays.

E. coli strain K27 contains a mutation in the fadD gene impairing13-oxidation of fatty acids, which results in the accumulation of freefatty acids in the growth medium (Klein et al., Eur. J. Biochem. 19:442-450 (1971); and Overath et al., Eur. J. Biochem. 7: 559-574 (1969)).Each TE was expressed in E. coli K27, and free fatty acids thataccumulated in the medium were extracted and analyzed. Four colonies foreach construct were independently cultured in 2 mL LB mediumsupplemented with 100 mg/L carbicillin in 17-mL culture tubes. When theculture reached an OD₆₀₀ of ˜0.7, the growth medium was replaced with 3mL of M9 minimal medium (47.7 mM Na₂HPO₄, 22.1 mM KH₂PO₄, 8.6 mM NaCl,18.7 mM NH₄C1, 2 mM MgSO₄, and 0.1 mM CaCl₂) supplemented with 0.4%glucose and 100 mg/l carbicillin, and 10 μMisopropyl-β-D-thiogalactopyranoside (IPTG) was added to induce acyl-ACPTE expression. After 40 hours of cultivation, cells were pelleted, andfree fatty acids in the supernatant were extracted essentially followinga previously described method (Voelker et al., J. Bacteriol. 176:7320-7327 (1994); and Mayer et al., BMC Plant Biol. 2007: 7 (2007)).Briefly, 2 mL of culture supernatant was supplemented with 10 μgheptanoic acid (7:0), 10 μg undecanoic acid (11:0), and 20 μgheptadecanoic acid (17:0) (Sigma-Aldrich, St. Louis, Mo., USA) asinternal standards. The mixture was acidified with 20 μL of 1 M HCl, and4 mL chloroform-methanol (1:1 vol/vol) was used to recover the fattyacids from the medium. After vortexing for 10 minutes and centrifugingat 1000×g for four minutes, the lower chloroform phase was transferredto a new tube and evaporated under a stream of N₂ gas until the sampleswere concentrated to ˜300 μL. Samples (1 μL) were analyzed on an AgilentTechnologies (Santa Clara, Calif., USA) 6890 Series gas chromatograph(GC) system used with an Agilent 5973 mass selective detector equippedwith an Agilent CP-Wax 58 FFAP CB column (25 mm×0.15 mm×0.39 mm). The GCprogram followed an initial temperature of 70° C. for two minutes,ramped to 150° C. at 10° C./minute and held for three minutes, ramped to260° C. at 10° C./minute, and held for 14 minutes. Final quantificationanalysis was performed with AMDIS software (National Institute ofStandards and Technology). Determination of C4 to C8, C10 to C12,and >C12 fatty acid concentrations was based on the fatty acid internalstandards 7:0, 11:0, and 17:0, respectively. The total concentration offatty acids produced by each acyl-ACP TE was obtained by subtracting theconcentration of fatty acid produced by E. coli expressing a controlplasmid (pUC57) lacking a TE from that produced by E. coli expressing agiven acyl-ACP TE sequence from the same vector. The three most abundantfatty acids produced by the control strain were 8:0 (2.0 nmol/ml), 14:0(3.5 nmol/ml), and 16:0 (3.1 nmol/ml), and their levels were minimalcompared to strains expressing acyl-ACP TEs. Compared to GC analyses offatty acids after derivatization (e.g., methylation or butylation), theGC-MS method used non-derivatized free fatty acids, which is betteroptimized for analyzing short-chain fatty acids (e.g., 4:0, 6:0, 8:0,10:0, 12:0, and 14:0). However, this method may be less sensitive forlonger-chain fatty acids (e.g., 18:0 and 18:1).

Analysis of free fatty acids revealed possible peaks characteristic of2-tridecanone. To further confirm this identification, retention timesand MS spectra of the peaks in each sample were compared to a2-tridecanone standard (Sigma-Aldrich).

All isolated acyl-ACP TE cDNAs were expressed in E. coli strain K27.Secreted fatty acids were analyzed with GC-MS, and the total fatty acidyield in the medium was used to represent the in vivo activities ofthese enzymes on acyl-ACPs, though it remains possible that some ofthese enzymes might also hydrolyze acyl-CoAs (Othman et al., Biochem.Soc. Trans. 28: 619-622 (2000)).

A total of 13 acyl-ACP TEs from Subfamily A were characterized,including single acyl-ACP TEs from Cuphea palustris (GenBank:AAC49179),U. americana (GenBank:AAB71731), and oil palm (E. guineensis,GenBank:AAD42220), two each from Iris germanica (GenBank:AAG43857 andGenBank:AAG43858) and Sorghum bicolor (GenBank:EER87824 andGenBank:EER88593), and three each from coconut and C. viscosissima.Total fatty acid concentrations produced by these acyl-ACP TEs arelisted in Table 1, and the resulting fatty acid compositions are shownin FIG. 2. Acyl-ACP TEs from C. palustris and U. americana, which havepreviously been functionally characterized in vitro (Dehesh et al.(1996), supra; and Voelker et al. (1997), supra), were studied ascontrols.

C. palustris acyl-ACP TE produced 97 mol % 8:0 and only 0.8 mol % 10:0fatty acids (FIG. 2A), while U. americana acyl-ACP TE made 44 mol % 8:0and 23 mol % 10:0 fatty acids (FIG. 2B). E. guineensis acyl-ACP TEproduced mainly 14:0 (47 mol %) and 16:1 (26 mol %) fatty acids (FIG.2C). The acyl-ACP TEs from I. germanica and S. bicolor have similarsubstrate specificities, producing mainly 14:0 (30-46 mol %), 16:0(11-23 mol %), and 16:1 (31-44 mol %) fatty acids (FIG. 2B). CnFatB1(JF338903) and CnFatB2 (JF338904) made predominantly 14:0 (36-44 mol %)and 16:1 (31-44 mol %) fatty acids, whereas CnFatB3 (JF338905) mademainly 12:0 (34 mol %) and 14:1 (22 mol %) fatty acids (FIG. 2C).Finally, CvFatB1 (JF338906) produced mainly 8:0 (51 mol %) and 10:0 (25mol %), and CvFatB2 (JF338907) made mainly 14:0 (46 mol %), 16:0 (25 mol%) and 16:1 (20 mol %) fatty acids (FIG. 2A). In contrast, CvFatB3(JF338908) has narrower substrate specificity, producing predominantly14:0 fatty acid (84 mol %).

The CvFatB1 and CvFatB3 TEs, for which corresponding cDNAs were isolatedfrom the developing seeds of C. viscosissima produced MCFAs in E. coli,and CvFatB1 shows substrate specificity consistent with the fatty acidconstituents present in the seed oil. The relative distributions of 8:0and 10:0 fatty acids differ; CvFatB1 produced twice as much 8:0 comparedto 10:0 fatty acid, whereas there is ˜fourfold more 10:0 fatty acidwithin C. viscosissima seed oil (Phippen et al., Ind. Crop Prod. 24:52-59 (2006)).

Three acyl-ACP TEs from plant sources belonging to Subfamily B,including those from P. patens (GenBank:EDQ65090) and S. bicolor(GenBank:EER96252 and GenBank:EES11622), and one acyl-ACP TE fromSubfamily D sourced from the alga Micromonas pusilla (GenBank:EEH52851),were similarly characterized. Total activity in E. coli expressing theseacyl-ACP TEs varied from 9 to 380 nmol/mL (Table 1). These four acyl-ACPTEs showed similar substrate specificities, producing predominantly 14:0(34-65 mol %) and 16:1 (23-37 mol %) fatty acids (FIG. 2D).

Eleven acyl-ACP TE sequences from Subfamilies E to J sourced frombacteria and three bacterial sequences that were not placed in anysubfamily were characterized (Table 1 and FIG. 3). Based on theirsubstrate specificities, these acyl-ACP TEs were classified into twogroups. One group produced primarily SCFAs and MCFAs (>75 mol % 4:0 to8:0 fatty acids). This group included acyl-ACP TEs from Anaerococcustetradius (GenBank:EEI82564, no subfamily, 87% 8:0), Clostridiumperfringens (GenBank:ABG82470, Subfamily G, 14% 6:0 and 70% 8:0),Lactobacillus brevis (GenBank:ABJ63754, Subfamily J, 7% 4:0, 14% 6:0,and 55% 8:0), and Lactobacillus plantarum (GenBank:CAD63310, SubfamilyJ, 11% 6:0 and 68% 8:0) (FIG. 3). The other group showed broad- andbinary-range substrate specificities. The binary-range activities werecentered on C8 and C12/C14 substrates (FIG. 3).

Interestingly, many bacterial acyl-ACP TEs, such as those fromDesulfovibrio vulgaris (GenBank:ACL08376, Subfamily E), L. brevis(GenBank:ABJ63754, Subfamily J), L. plantarum (GenBank:CAD63310,Subfamily J), and Bdellovibrio bacteriovorus (GenBank:CAE80300, nosubfamily), are part of the pathway that produces noticeable amounts ofthe methylketone 2-tridecanone through enzymatic hydrolysis of3-keto-tetradecanoyl-ACP followed by chemical decarboxylation. B.bacteriovorus acyl-ACP TE produced the highest concentration of2-tridecanone, 9.4 nmol/mL (FIG. 4), which was 3 mol % of the fattyacids produced.

The accumulation of both unsaturated fatty acids and saturated fattyacids observed is consistent with the previous conclusion that theheterologously expressed acyl-ACP TEs can intercept both saturated andunsaturated intermediates of fatty acid biosynthesis of E. coli(Magnuson et al., Microbiol. Rev. 57: 522-542 (1993)). Interestingly, inthe E. coli heterologous expression system used, six bacterial-sourcedacyl-ACP TEs and three plant-sourced acyl-ACP TEs produced noticeableamounts (>1 nmol/mL) of methylketones, largely 2-tridecanone. Theacyl-ACP TE from B. bacteriovorus (GenBank: CAE80300) produced thehighest concentration of 2-tridecanone (9.4 nmol/mL).

Methylketones, such as 2-tridecanone, occur in the wild tomato speciesSolanum habrochaites subsp. Glabratum (Antonious, J. Environ. Sci.Health B 36: 835-848 (2001)), and their biosynthesis is catalyzed by twosequentially-acting methylketone synthases, MKS1 and MKS2. MKS2 is athioesterase that catalyzes the hydrolysis of the 3-ketoacyl-ACPintermediate in fatty acid biosynthesis, and MKS1 catalyzes thedecarboxylation of the released 3-keto acid to produce a methylketone(Ben-Israel et al., Plant Physiol. 151: 1952-1964 (2009); and Yu et al.,Plant Physiol. 154: 67-77 (2010)). Heterologous expression of MKS2 in E.coli yields many methylketones, including 2-tridecanone (Yu et al.(2010), supra). However, MKS2 is not included in Family TE14; rather, itis included in Family TE9 (Cantu et al. (2010), supra). Although someFamily TE14 members share very low, if any, significant sequencesimilarity (i.e., <15% identity) to MKS2, the data indicate that atleast nine acyl-ACP TEs (e.g., B. bacteriovorus, GenBank:CAE80300) cancatalyze the same reaction as MKS2 (i.e, hydrolysis of the thioesterbond of 3-ketoacyl-ACP), and that the resulting product (3-keto acid) isfurther chemically or enzymatically decarboxylated to generate themethylketone.

Example 4

This example describes statistical cluster analysis.

To classify acyl-ACP TEs based on their in vivo activities, the fattyacid composition data obtained from the in vivo expression of all TEsequences studied were used to perform statistical clustering analysis.The distance matrix was calculated using Euclidean distances, and Ward'smethod (Ward, J. Am. Stat. Assoc. 58: 236 (1963)) was used to performagglomerative hierarchical clustering. The p-values were calculated viamultiscale bootstrap re-sampling with 1,000 replicates (Suzuki et al.,Bioinformatics 22: 1540-1542 (2006)).

All acyl-ACP TEs that were characterized were clustered into threeclasses: 1) Class I contains acyl-ACP TEs that mainly act on C14 and C16substrates; 2) Class II has acyl-ACP TEs that have broad substratespecificities, with major activities toward C8 and C14 substrates; and3) Class III comprises acyl-ACP TEs that predominantly act on C8substrate (FIG. 5). Class I consists of thirteen plant acyl-ACP TEs fromSubfamilies A, B, and D. Class II contains eleven acyl-ACP TEs, ten frombacteria in Subfamilies E, F, H, I, and J, and a non-grouped sequence,and only one from a plant (CnFatB3) in Subfamily A. Class III includesseven acyl-ACP TEs, of which three are from plants in Subfamily A andfour are from bacteria in Subfamilies G and J and a non-groupedsequence. Considering the previously characterized class of oleoyl-ACPTEs in Subfamily C, TE14 members may now be sorted into four classesbased on their substrate specificities.

Comparison between the specificity-based classification and thesequence-based phylogenetic tree indicates that the two classificationsare not necessarily consistent with each other. Three phenomena wereobserved in this study. First, diverged sequences (variants in primarystructure) from the same species do not necessarily differ in function.Second, similar sequences may have different substrate specificities.Third, sequences that belong to different subfamilies because they sharelow sequence identity can have very similar substrate specificities.Therefore, it is not reasonable to infer the substrate specificity ofone acyl-ACP TE based on its sequence-based classification within thesame subfamily. It is conceivable, therefore, that the change ofsubstrate specificity is most likely caused by changes of only a fewamino acid residues, and that many different combinations of residuechanges could result in changed specificities (Jones (1995), supra).Bacterial orthologs provide access to additional functional diversity,both relative to acyl chain length specificity (e.g., shorter acylchains, as short as four carbon atoms), as well as acyl chains thatcontain additional chemical functionalities (e.g., unsaturated acylchains and acyl chains containing carbonyl groups).

Example 5

This example describes the generation of random mutants andsite-directed mutants of acyl-ACP TE EET61113.

DNA sequences for the wild-type acyl-ACP TE EET61113 was synthesized andcloned into pUC57 vector as previously. The random mutants weregenerated by error-prone PCR using primers designed on pUC57 vector(pUC57F: 5′-CTGCAAGGCGATTAAGTTGGGTAAC-3′ [SEQ ID NO: 11]; pUC57R:5′-CGGCTCGTATGTTGTGTGGAAT-3′ [SEQ ID NO: 12]). The PCR was conducted in40 tubes of reaction mixture (15 μl), which contained 1×PCR buffer, 0.2mM dATP and dGTP, 1 mM dCTP and dTTP, 7 mM MgCl₂, 0.1 mM MnCl₂, 0.5 μlof each primers, 1.5 ng plasmid containing the thioesterase gene, and0.15 U Taq DNA polymerase (Invitrogen), using a cycling program of 94°C. for 4 minutes, 31 cycles of 94° C. for 30 seconds, 52° C. for 30seconds, and 72° C. for 1 minute, and a final extension step of 72° C.for 5 minutes. The PCR products were pooled together, purified with theQiaQuick gel extraction kit (Qiagen, Valencia, Calif., USA), digestedwith Bam HI and Eco RI, and then cloned into the correspondingrestriction sites of the pUC57 vector. The constructed vectorscontaining mutant genes were transformed into E. coli K27 byelectroporation.

Site-directed mutations were also introduced into wild-type acyl-ACP TEEET61113. Specifically, a mutant (designated TE20-N169Y), which containsa single N->Y mutation at amino acid position 169, and another mutant(designated TE20-S222I), which contains a single S->I mutation at aminoacid position 222, were generated.

Example 6

This example describes the initial screening of acyl-ACP TE mutantsgenerated in Example 5.

Mutants were screened on Neutral Red-containing media, which was M9minimal medium (47.7 mM Na₂HPO₄, 22.1 mM KH₂PO₄, 8.6 mM NaCl, 18.7 mMNH₄C1, 2 mM MgSO₄, and 0.1 mM CaCl₂) solidified by 15 g/L agar andsupplemented with 0.4% glucose, 100 mg/L carbicillin, 1 mM IPTG, and 40ppm Neutral Red. This screening method is based on pH change in themedia. Mutants with higher acyl-ACP TE activity will produce more freefatty acids, which decrease the pH of the colonies and generate a moreintense red color. Briefly, after electroporation, an appropriate amountof culture was spread on the Neutral Red plates so that each plate wouldcontain 100-200 colonies. The plates were incubated at 30° C. for twodays, and then at room temperature for another 3-5 days. Eventually, thecolonies that are more intensely red were selected for furthercharacterization with GC-MS.

Example 7

This example describes the further characterization of those mutantsthat were identified in Example 6 as producing more fatty acids.

Colonies that were more intensely red on the Neutral Red plate wereassumed to produce more fatty acids. The activity and composition of themutants were characterized as described above with slight modification.Instead of 20 μl of 1 M HCl, 200 μl of 1 M HCl were used to acidify thecell culture supernatant, which allowed recovery of more butanoic acidfrom the sample. Thus, the activity of wild-type thioesterase EET61113in this Example was higher than the production in the above Examples.

The in vivo activities of 139 mutants have been determined so far. Theirtotal activitys are shown in FIG. 2. The data of all mutants (blue bars)were from single analysis, while the activity of EET61113 (red bar) waspresented as the average of 16 replicates. A total of 27 mutants showedhigher acyl-ACP TE activity than wild-type, among which 8 mutants showedmore than 20% increase and 2 mutants (TE20MT156 and TE20MT180) had ˜40%increase. While activity increased slightly in the site-directed mutantsTE20-N169Y and TE20-S222I as compared to wild-type EET61113, activityincreased dramatically in a random mutant (designated TE20MT9)containing the N169Y and S222I mutations. Thus, surprisingly the doublemutation had a synergistic effect, as opposed to an additive effect, onactivity by the mutant acyl-ACP TE. While the wild-type TE producedapproximately 50 nmol/ml culture of 4:0 fatty acids and approximately110 nmol/ml culture of 6:0 fatty acids, the mutant designated TE20MT9produced approximately 45 nmol/ml culture of 4:0 fatty acids andapproximately 230 nmol/ml culture of 6:0 fatty acids.

Example 8

This example describes the construction of chimeric TEs.

CvFatB1 and CvFatB2 share 72% identity in their amino acid sequences,but have very different substrate specificities: CvFatB1 mainly producesC8 and C10 fatty acids, while CvFatB2 produces C14 and C16 fatty acids.Chimeric TEs were constructed using these two sequences to locate theregion(s) that determine the substrate specificity of acyl-ACP TEs.Previously, CvFatB1 and CvFatB2 genes were codon-optimized, synthesized,and cloned into the pUC57 vector. Using the primers listed in Table 3,six fragments (I, II, III, IV, V, and VI) for each TE gene weregenerated (see FIG. 7).

TABLE 3 Primers for amplification of the fragments I through VIFragments Forward primer Reverse primer IpUC57R (5′-CGGCTCGTATGTTGTGTGGAAT-3′)Cv-R2 (5′-GGTACGATCCGCGCCGATTTC-3′) [SEQ ID NO: 12] [SEQ ID NO: 18] IICv-F2 (5′-GAAATCGGCGCGGATCGTACC-3′) Cv-R3 (5′-CCAGGTCGGATAACGATTGAC-3′)[SEQ ID NO: 13] [SEQ ID NO: 19] III Cv-F3 (5′-GTCAATCGTTATCCGACCTGG-3′)Cv-R4 (5′-CGGGTTTTCTGGTTCATCAT-3′) [SEQ ID NO: 14] [SEQ ID NO: 20] IVCv-F4 (5′-ATGATGAACCAGAAAACCCG-3′) Cv-R5 (5′-TCGTTCCAACGCGGCGTCAGACC-3′)[SEQ ID NO: 15] [SEQ ID NO: 21] V Cv-F5 (5′-GGTCTGACGCCGCGTTGGAACGA-3′)Cv-R6 (5′-ATCTTCCAGACGCAGCAG-3′) [SEQ ID NO: 16] [SEQ ID NO: 22] VICv-F6 (5′-CTGCTGCGTCTGGAAGAT-3′)pUC57F (5′-CTGCAAGGCGATTAAGTTGGGTAAC-3′) [SEQ ID NO: 17] [SEQ ID NO: 11]

The chimeric TEs were constructed by re-assembling the six fragments torecreate the full-length thioesterase gene sequence by PCR, using acombination of fragments from either CvFatB1 or CvFatB2. PCR wasperformed in a 50-μL reaction mixture containing 10 ng of each fragment,1× Phusion buffer, 0.2 mM dNTP, 0.5 μM pUC57F and pUC57R primers, and 1Unit of Phusion high-fidelity DNA polymerase (New England Biolabs) usinga cycling program of 98° C. for 2 minutes, 32 cycles of 98° C. for 10seconds, 50° C. for 15 seconds, and 72° C. for 20 seconds, and a finalextension step of 72° C. for 5 minutes. The expected full-length geneproducts were identified by agarose gel electrophoresis, recovered fromthe gel using the QiaQuick gel extraction kit (Qiagen, Valencia, Calif.)and cloned into the pUC57 vector using the Bam HI and Eco RI restrictionsites. The sequence of each construct was confirmed by sequencing usingprimers pUC57F and pUC57R.

Example 9

This example describes the use of sequence alignments to identifycatalytic residues.

A total of 27 representative acyl-ACP TE sequences, including both plantand bacterial TEs that were previously functionally characterized, werealigned using Vector NTI software (Invitrogen) with the defaultparameters. While Cysteine 264 was previously proposed to be a catalyticresidue by Mayer et al. (J. Biol. Chem. 280: 3621-3627 (2005)), Cys264was not conserved among these 27 TE sequences. The adjacent glutamicacid (Glu263), however, was conserved and predicted to be a catalyticresidue. Multiple sequence alignment and phylogenetic analysis resultedin the identification of another nine residues that also may affectsubstrate specificities, namely residue 110 in Fragment II, residues 133and 139 in Fragment III, and residues 173, 176, 184, 192, 198, and 205in Fragment IV (see FIG. 9, which lists the amino acid present at agiven position for the indicated organism). The presence of leucine (L)or valine (V) at position 110, phenylalanine (F) or leucine (L) atposition 133, isoleucine (I) at position 139, phenylalanine (F) orleucine (L) at position 173, leucine (L) at position 176, isoleucine(I), phenylalanine (F) or leucine (L) at position 184, proline (P) atposition 192, asparagine (N) or serine (S) at position 198, andphenylalanine (F) at position 205 were associated with the production ofmainly C8 fatty acids. The production of mainly C14/16 fatty acids wasassociated with the presence of valine (V) or leucine (L) at position110, valine (V) or alanine (A) at position 133, asparagine (N) atposition 139, leucine (L) at position 173, isoleucine (I), phenylalanine(F), valine (V), or methionine (M) at position 176, isoleucine (I; or,in one instance, leucine (L)) at position 184, threonine (T), serine(S), valine (V), alanine (A), proline (P), or aspartic acid (D) atposition 192, aspartic acid (D) at position 198, and leucine (L) atposition 205. Site-directed mutagenesis and fatty acid profiling wereused for verification.

Example 10

This example describes the use of site-directed mutagenesis to verifycatalytic residues.

Point mutants were generated from CvFatB2 with the QuikChange IIsite-directed mutagenesis kit (Agilent Technologies) according tomanufacturer's instructions in order to test whether the predictedresidues, which were identified in Example 9, affected the substratespecificity of acyl-ACP TEs. The residues of CvFatB2 were mutated to thecorresponding residues in CvFatB1 with the exception of residues valine110 (V110) and isoleucine 184 (1184), which were mutated to the bulkierresidue, phenylalanine. The point mutations were introduced sequentiallyfor the mutants that harbored multiple amino acid changes. All mutantswere confirmed by sequencing. The results are shown in FIG. 10, whichshows the fatty acid profiles of the mutants on the right (wherein thegreen color highlights the major fatty acids produced by the TEs), thecluster analysis of the fatty acid profiles on the left, and the pointmutations in each mutant in the middle. The wild-type enzyme is CvFatB2,which is shown in the color blue. The color orange indicates residuesthat have been mutated to the amino acid present at the correspondingposition in CvFatB1. Red points indicate residues that have been mutatedto amino acids that are not present in CvFatB1 or CvFatB2.

Example 11

This example describes the production of fatty acids in vivo by TEvariants.

TE variants were analyzed in accordance with the method of Example 3.The results are shown in FIGS. 8 a and 8 b. As shown in FIGS. 8 a and 8b, the biggest variances among the chimeric TEs were observed for 8:0and 14:0 fatty acids. The mole percentages of 8:0 and 14:0 fatty acidsfor all chimeric TEs were plotted, and it was determined that thereplacement of Fragment III changed the fatty acid profile mostdramatically. Thus, Fragment III was determined to contain the mostimportant residues for substrate specificity, although Fragments I, II,and IV also affected substrate specificity.

Thus, in view of the above, the present invention provides thefollowing:

A. A method of increasing production of fatty acids in a host cell ororganism, which method comprises introducing into the host cell ororganism and expressing therein a nucleic acid molecule comprising anucleotide sequence encoding an acyl-acyl carrier protein (ACP)thioesterase (TE) from Bryantella formatexigens, whereupon theproduction of fatty acids in the host cell or organism is increased.

B. The method of A, wherein the host cell or organism is a bacterium, ayeast, an alga, or a crop plant.

C. A method of increasing production of short-chain fatty acids in ahost cell or organism, which method comprises introducing into the hostcell or organism and expressing therein a nucleic acid moleculecomprising a nucleotide sequence encoding a mutant acyl-ACP TE derivedfrom wild-type Bryantella formatexigens acyl-ACP TE, whereupon theproduction of short-chain fatty acids in the host cell or organism isincreased and wherein the mutant acyl-ACP TE produces more short-chainfatty acids in the host cell or organism than the correspondingwild-type acyl-ACP TE.

D. The method of C, wherein the mutant acyl-ACP TE differs fromwild-type Bryantella formatexigens acyl-ACP TE by two or more amino acidmutations comprising N169Y and S222I and wherein the mutant acyl-ACP TEhas increased thioesterase activity compared to wild-type Bryantellaformatexigens acyl-ACP TE.

E. The method of C, wherein the host cell or organism is a bacterium, ayeast, an alga, or a crop plant.

F. The method of D, wherein the host cell or organism is a bacterium, ayeast, an alga, or a crop plant.

G. A method of making a mutant Bryantella formatexigens acyl-ACP TE,which method comprises making a mutant Bryantella formatexigens acyl-ACPTE comprising two or more amino acid mutations comprising N169Y andS222I, whereupon a mutant Bryantella formatexigens acyl-ACP TE is made.

H. The method of G, wherein the mutant Bryantella formatexigens acyl-ACPTE has increased thioesterase activity compared to a correspondingwild-type Bryantella formatexigens acyl-ACP TE.

I. An isolated or purified nucleic acid molecule comprising a nucleotidesequence encoding a mutant acyl-ACP TE, which is derived from wild-typeBryantella formatexigens acyl-ACP TE, comprises two or more amino acidmutations comprising N169Y and S222I, and has increased thioesteraseactivity compared to wild-type Bryantella formatexigens acyl-ACP TE,wherein the isolated or purified nucleic acid molecule can be a vector.

J. A host cell or organism comprising the isolated or purified nucleicacid molecule of I.

K. The host cell or organism of J, wherein the host cell or organism isa bacterium, a yeast, an alga, or a crop plant.

L. An isolated or purified mutant acyl-ACP TE, which is derived fromwild-type Bryantella formatexigens acyl-ACP TE, comprises two or moreamino acid mutations comprising N169Y and S222I, and has increasedthioesterase activity compared to wild-type Bryantella formatexigensacyl-ACP TE.

M. A method of making a chimeric Cuphea viscosissima acyl-ACP TE, whichmethod comprises replacing a segment of a wild-type Cuphea viscosissimaacyl-ACP TE with a segment of another acyl-ACP TE, whereupon a chimericCuphea viscosissima acyl-ACP TE is made.

N. The method of M, wherein the segment of another acyl-ACP TE gene is asegment of another Cuphea viscosissima acyl-ACP TE.

O. The method of M, which method comprises replacing a segment of awild-type Cuphea viscosissima FatB1 (CvFatB1) gene with a segment ofanother acyl-ACP TE gene to produce a chimeric CvFatB1 gene or replacinga segment of a wild-type Cuphea viscosissima FatB2 (CvFatB2) gene with asegment of another acyl-ACP TE gene to produce a chimeric CvFatB2 gene.

P. The method of O, which method comprises replacing a segment of awild-type CvFatB1 gene with a segment of a CvFatB2 gene to produce achimeric CvFatB1 gene or replacing a segment of a wild-type CvFatB2 genewith a segment of a CvFatB1 gene to produce a chimeric CvFatB2 gene.

Q. The method of M, wherein the chimeric Cuphea viscosissima acyl-ACP TE(i) has a substrate specificity that differs from the correspondingwild-type Cuphea viscosissima acyl-ACP TE, (ii) produces a total amountof fatty acids that differs from the total amount of fatty acidsproduced by the corresponding wild-type Cuphea viscosissima acyl-ACP TE,or (iii) has a substrate specificity and produces a level of a fattyacid, both of which differ from the corresponding wild-type Cupheaviscosissima acyl-ACP TE.

R. An isolated or purified nucleic acid molecule comprising a nucleotidesequence encoding a chimeric Cuphea viscosissima acyl-ACP TE gene, whichcomprises a segment of another acyl-ACP TE gene, wherein the isolated orpurified nucleic acid molecule can be a vector.

S. The isolated or purified nucleic acid molecule of R, wherein thesegment of another acyl-ACP TE gene is a segment of another Cupheaviscosissima acyl-ACP TE gene.

T. The isolated or purified nucleic acid molecule of R, wherein thechimeric Cuphea viscosissima acyl-ACP TE gene is a chimeric FatB1 geneor a chimeric FatB2 gene.

U. The isolated or purified nucleic acid molecule of T, wherein thechimeric Cuphea viscosissima acyl-ACP TE gene is a chimeric FatB1 genecomprising a segment of a Cuphea viscosissima FatB2 gene or the chimericCuphea viscosissima acyl-ACP TE gene is a chimeric FatB2 gene comprisinga segment of a Cuphea viscosissima FatB1 gene.

V. A host cell or organism comprising the isolated or purified nucleicacid molecule of R-U.

W. An isolated or purified chimeric Cuphea viscosissima acyl-ACP TE,which comprises a segment of another acyl-ACP TE.

X. The isolated or purified chimeric Cuphea viscosissima acyl-ACP TE ofW,

wherein the segment of another acyl-ACP TE is a segment of anotherCuphea viscosissima acyl-ACP TE.

Y. The isolated or purified chimeric Cuphea viscosissima acyl-ACP TE ofW, which is a chimera of the TE encoded by a FatB1 gene or a chimera ofthe TE encoded by a FatB2 gene.

Z. The isolated or purified chimeric Cuphea viscosissima acyl-ACP TE ofY, which is a chimera of the TE encoded by a FatB1 gene comprising asegment of the TE encoded by a FatB2 gene or a chimera of the TE encodedby a FatB2 gene comprising a segment of the TE encoded by a FatB1 gene.

AA. A method of altering the specificity of a plant acyl-ACP TE for atleast one of its substrates, which method comprises introducing into theplant acyl-ACP TE a substrate specificity-altering mutation in theregion corresponding to amino acids 118-167 of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2,whereupon the specificity of the plant acyl-ACP TE for at least one ofits substrates is altered.

AB. The method of AA, which comprises mutating at least one amino acidcorresponding to an amino acid selected from the group consisting ofamino acid 133, amino acid 142, and amino acid 143 of the mature aminoacid sequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AC. The method of AB, which further comprises mutating at least oneamino acid corresponding to an amino acid selected from the groupconsisting of amino acid 110 and amino acid 184 of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AD. The method of AA, which further comprises altering the level ofactivity of the plant acyl-ACP TE by a method comprising mutating atleast one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 173, amino acid 176, and amino acid 205of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2, whereupon the level of activity of the plant acyl-ACPTE is altered.

AE. The method of AB, which further comprises altering the level ofactivity of the plant acyl-ACP TE by a method comprising mutating atleast one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 173, amino acid 176, and amino acid 205of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2, whereupon the level of activity of the plant acyl-ACPTE is altered.

AF. The method of AC, which further comprises altering the level ofactivity of the plant acyl-ACP TE by a method comprising mutating atleast one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 173, amino acid 176, and amino acid 205of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2, whereupon the level of activity of the plant acyl-ACPTE is altered.

AG. A method of altering the level of activity of a plant acyl-ACP TE,which method comprises mutating at least one amino acid corresponding toan amino acid selected from the group consisting of amino acid 173,amino acid 176, and amino acid 205 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2, whereupon thelevel of activity of the plant acyl-ACP TE is altered.

AH. The method of AG, which further comprises altering the specificityof the plant acyl-ACP TE for at least one of its substrates by a methodcomprising introducing into the plant acyl-ACP TE a substratespecificity-altering mutation in the region corresponding to amino acids118-167 of the mature amino acid sequence of the Cuphea viscosissimaacyl-ACP TE encoded by FatB2, whereupon the specificity of the plantacyl-ACP TE for at least one of its substrates is altered.

AI. The method of AH, which comprises mutating at least one amino acidselected from the group consisting of amino acid 133, amino acid 142,and amino acid 143 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2.

AJ. The method of AI, which further comprises mutating at least oneamino acid corresponding to an amino acid selected from the groupconsisting of amino acid 110 and amino acid 184 of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AK. An isolated or purified nucleic acid molecule comprising anucleotide sequence encoding a mutant plant acyl-ACP TE, which comprisesa substrate specificity-altering mutation in the region corresponding toamino acids 118-167 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2, wherein the isolated orpurified nucleic acid molecule can be a vector.

AL. The isolated or purified nucleic acid molecule of AK, wherein themutant plant acyl-ACP TE comprises a mutation of at least one amino acidcorresponding to an amino acid selected from the group consisting ofamino acid 133, amino acid 142, and amino acid 143 of the mature aminoacid sequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AM. The isolated or purified nucleic acid molecule of AL, wherein themutant plant acyl-ACP TE further comprises a mutation of at least oneamino acid corresponding to an amino acid selected from the groupconsisting of amino acid 110 and amino acid 184 of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AN. The isolated or purified nucleic acid molecule of AK-AM, wherein themutant plant acyl-ACP TE further comprises a level of activity-alteringmutation of at least one amino acid corresponding to an amino acidselected from the group consisting of amino acid 173, amino acid 176,and amino acid 205 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2.

AO. An isolated or purified nucleic acid molecule comprising anucleotide sequence encoding a mutant plant acyl-ACP TE, which comprisesa level of activity-altering mutation of at least one amino acidcorresponding to an amino acid selected from the group consisting ofamino acid 173, amino acid 176, and amino acid 205 of the mature aminoacid sequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2,wherein the isolated or purified nucleic acid molecule can be a vector.

AP. The isolated or purified nucleic acid molecule of AO, wherein themutant plant acyl-ACP TE further comprises a substratespecificity-altering mutation in the region corresponding to amino acids118-167 of the mature amino acid of the Cuphea viscosissima acyl-ACP TEencoded by FatB2.

AQ. The isolated or purified nucleic acid molecule of AP, wherein themutant plant acyl-ACP TE comprises a mutation of at least one amino acidcorresponding to an amino acid selected from the group consisting ofamino acid 133, amino acid 142, and amino acid 143 of the mature aminoacid sequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AR. The isolated or purified nucleic acid molecule of AQ, wherein themutant plant acyl-ACP TE further comprises a substratespecificity-altering mutation of at least one amino acid correspondingto an amino acid selected from the group consisting of amino acid 110and amino acid 184 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2.

AS. A host cell or organism comprising the isolated or purified nucleicacid molecule of AK-AR.

AT. An isolated or purified mutant plant acyl-ACP TE, which comprises asubstrate specificity-altering mutation in the region corresponding toamino acids 118-167 of the mature amino acid sequence of the Cupheaviscosissima acyl-ACP TE encoded by FatB2.

AU. The isolated or purified mutant plant acyl-ACP TE of AT, whichcomprises a mutation of at least one amino acid corresponding to anamino acid selected from the group consisting of amino acid 133, aminoacid 142, and amino acid 143 of the mature amino acid sequence of theCuphea viscosissima acyl-ACP TE encoded by FatB2.

AV. The isolated or purified mutant plant acyl-ACP TE of AU, whichfurther comprises a substrate specificity-altering mutation of at leastone amino acid corresponding to an amino acid selected from the groupconsisting of amino acid 110 and amino acid 184 of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AW. The isolated or purified mutant plant acyl-ACP TE of AT-AV, whichfurther comprises a level of activity-altering mutation of at least oneamino acid corresponding to an amino acid selected from the groupconsisting of amino acid 173, amino acid 176, and amino acid 205 of themature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2.

AX. An isolated or purified mutant plant acyl-ACP TE, which comprises alevel of activity-altering mutation of at least one amino acidcorresponding to an amino acid selected from the group consisting ofamino acid 173, amino acid 176, and amino acid 205 of the mature aminoacid sequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AY. The isolated or purified mutant plant acyl-ACP TE of claim AX, whichfurther comprises a substrate specificity-altering mutation in theregion corresponding to amino acids 118-167 of the mature amino acid ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2.

AZ. The isolated or purified mutant plant acyl-ACP TE of claim AY, whichcomprises a mutation of at least one amino acid corresponding to anamino acid selected from the group consisting of amino acid 133, aminoacid 142, and amino acid 143 of the mature amino acid sequence of theCuphea viscosissima acyl-ACP TE encoded by FatB2.

BA. The isolated or purified mutant plant acyl-ACP TE of claim AZ, whichfurther comprises a substrate specificity-altering mutation of at leastone amino acid corresponding to an amino acid selected from the groupconsisting of amino acid 110 and amino acid 184 of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2.

All references, including publications, patent applications, andpatents, cited herein are hereby incorporated by reference to the sameextent as if each reference were individually and specifically indicatedto be incorporated by reference and were set forth in its entiretyherein.

The use of the terms “a,” “an,” “the,” and similar referents in thecontext of describing the invention (especially in the context of thefollowing claims) are to be construed to cover both the singular and theplural, unless otherwise indicated herein or clearly contradicted bycontext. Recitation of ranges of values herein are merely intended toserve as a shorthand method of referring individually to each separatevalue falling within the range, unless otherwise indicated herein, andeach separate value is incorporated into the specification as if it wereindividually recited herein. All methods described herein can beperformed in any suitable order unless otherwise indicated herein orotherwise clearly contradicted by context. The use of any and allexamples, or exemplary language (e.g., “such as”) provided herein, isintended merely to illuminate better the invention and does not pose alimitation on the scope of the invention unless otherwise claimed. Nolanguage in the specification should be construed as indicating anynon-claimed element as essential to the practice of the invention.

Preferred embodiments of this invention are described herein, includingthe best mode known to the inventors for carrying out the invention. Itshould be understood that the illustrated embodiments are exemplaryonly, and should not be taken as limiting the scope of the invention.

1. A method of increasing production of fatty acids in a host cell ororganism, which method comprises introducing into the host cell ororganism and expressing therein a nucleic acid molecule comprising anucleotide sequence encoding an acyl-acyl carrier protein (ACP)thioesterase (TE) from Bryantella formatexigens, whereupon theproduction of fatty acids in the host cell or organism is increased. 2.A method of increasing production of short-chain fatty acids in a hostcell or organism, which method comprises introducing into the host cellor organism and expressing therein a nucleic acid molecule comprising anucleotide sequence encoding a mutant acyl-ACP TE derived from wild-typeBryantella formatexigens acyl-ACP TE, whereupon the production ofshort-chain fatty acids in the host cell or organism is increased andwherein the mutant acyl-ACP TE produces more short-chain fatty acids inthe host cell or organism than the corresponding wild-type acyl-ACP TE.3. A method of making a mutant Bryantella formatexigens acyl-ACP TE,which method comprises making a mutant Bryantella formatexigens acyl-ACPTE comprising two or more amino acid mutations comprising N169Y andS222I, whereupon a mutant Bryantella formatexigens acyl-ACP TE is made.4. An isolated or purified nucleic acid molecule comprising a nucleotidesequence encoding a mutant acyl-ACP TE, which is derived from wild-typeBryantella formatexigens acyl-ACP TE, comprises two or more amino acidmutations comprising N169Y and S222I, and has increased thioesteraseactivity compared to wild-type Bryantella formatexigens acyl-ACP TE,wherein the isolated or purified nucleic acid molecule can be a vector.5. A host cell or organism comprising the isolated or purified nucleicacid molecule of claim
 4. 6. An isolated or purified mutant acyl-ACP TE,which is derived from wild-type Bryantella formatexigens acyl-ACP TE,comprises two or more amino acid mutations comprising N169Y and S222I,and has increased thioesterase activity compared to wild-type Bryantellaformatexigens acyl-ACP TE.
 7. A method of making a chimeric Cupheaviscosissima acyl-ACP TE, which method comprises replacing a segment ofa wild-type Cuphea viscosissima acyl-ACP TE with a segment of anotheracyl-ACP TE, whereupon a chimeric Cuphea viscosissima acyl-ACP TE ismade.
 8. An isolated or purified nucleic acid molecule comprising anucleotide sequence encoding a chimeric Cuphea viscosissima acyl-ACP TEgene, which comprises a segment of another acyl-ACP TE gene, wherein theisolated or purified nucleic acid molecule can be a vector.
 9. A hostcell or organism comprising the isolated or purified nucleic acidmolecule of claim
 8. 10. An isolated or purified chimeric Cupheaviscosissima acyl-ACP TE, which comprises a segment of another acyl-ACPTE.
 11. A method of altering the specificity of a plant acyl-ACP TE forat least one of its substrates, which method comprises introducing intothe plant acyl-ACP TE a substrate specificity-altering mutation in theregion corresponding to amino acids 118-167 of the mature amino acidsequence of the Cuphea viscosissima acyl-ACP TE encoded by FatB2,whereupon the specificity of the plant acyl-ACP TE for at least one ofits substrates is altered.
 12. A method of altering the level ofactivity of a plant acyl-ACP TE, which method comprises mutating atleast one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 173, amino acid 176, and amino acid 205of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2, whereupon the level of activity of the plant acyl-ACPTE is altered.
 13. An isolated or purified nucleic acid moleculecomprising a nucleotide sequence encoding a mutant plant acyl-ACP TE,which comprises a substrate specificity-altering mutation in the regioncorresponding to amino acids 118-167 of the mature amino acid sequenceof the Cuphea viscosissima acyl-ACP TE encoded by FatB2, wherein theisolated or purified nucleic acid molecule can be a vector.
 14. Anisolated or purified nucleic acid molecule comprising a nucleotidesequence encoding a mutant plant acyl-ACP TE, which comprises a level ofactivity-altering mutation of at least one amino acid corresponding toan amino acid selected from the group consisting of amino acid 173,amino acid 176, and amino acid 205 of the mature amino acid sequence ofthe Cuphea viscosissima acyl-ACP TE encoded by FatB2, wherein theisolated or purified nucleic acid molecule can be a vector.
 15. A hostcell or organism comprising the isolated or purified nucleic acidmolecule of claim
 13. 16. A host cell or organism comprising theisolated or purified nucleic acid molecule of claim
 14. 17. An isolatedor purified mutant plant acyl-ACP TE, which comprises a substratespecificity-altering mutation in the region corresponding to amino acids118-167 of the mature amino acid sequence of the Cuphea viscosissimaacyl-ACP TE encoded by FatB2.
 18. An isolated or purified mutant plantacyl-ACP TE, which comprises a level of activity-altering mutation of atleast one amino acid corresponding to an amino acid selected from thegroup consisting of amino acid 173, amino acid 176, and amino acid 205of the mature amino acid sequence of the Cuphea viscosissima acyl-ACP TEencoded by FatB2.